Starting phenix.real_space_refine on Tue Jul 29 20:26:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qzx_18784/07_2025/8qzx_18784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qzx_18784/07_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_18784/07_2025/8qzx_18784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qzx_18784/07_2025/8qzx_18784.map" model { file = "/net/cci-nas-00/data/ceres_data/8qzx_18784/07_2025/8qzx_18784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qzx_18784/07_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-5711/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: 7.85, per 1000 atoms: 0.67 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: 2.67 Conformation dependent library (CDL) restraints added in 1.5 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: 1.21 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: 3.16 Time building geometry restraints manager: 3.18 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.900 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- 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= 1.095 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 Details of bonding type rmsd hydrogen bonds : bond 0.26141 ( 516) hydrogen bonds : angle 8.30060 ( 1494) covalent geometry : bond 0.01457 (11986) covalent geometry : angle 1.92327 (16266) *********************** 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 : 1.261 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: 0.2161 time to fit residues: 108.3919 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 : 1.273 ------------------------------------------------------------------------------- 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 = 0.178964 restraints weight = 14837.848| |-----------------------------------------------------------------------------| 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: 0.3976 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 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 = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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= 0.163 Angle : 0.656 9.803 16266 Z= 0.348 Chirality : 0.046 0.160 1785 Planarity : 0.005 0.069 2070 Dihedral : 13.244 85.975 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 Details of bonding type rmsd hydrogen bonds : bond 0.05863 ( 516) hydrogen bonds : angle 5.79074 ( 1494) covalent geometry : bond 0.00353 (11986) covalent geometry : angle 0.65607 (16266) *********************** 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 : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6311 (mtp) cc_final: 0.5458 (mmt) REVERT: A 155 HIS cc_start: 0.4187 (OUTLIER) cc_final: 0.3745 (m90) REVERT: B 47 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.4743 (mpt) REVERT: B 299 ARG cc_start: 0.5653 (ptp-110) cc_final: 0.4896 (tpt170) REVERT: B 328 SER cc_start: 0.7518 (t) cc_final: 0.7216 (p) REVERT: B 344 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5997 (tt0) REVERT: C 260 ASP cc_start: 0.7606 (t0) cc_final: 0.7388 (t70) REVERT: C 313 ASP cc_start: 0.7603 (p0) cc_final: 0.6495 (t0) REVERT: D 41 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7147 (t0) REVERT: D 145 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7322 (mt) REVERT: D 176 LYS cc_start: 0.7123 (tttt) cc_final: 0.6675 (tptp) REVERT: D 186 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7370 (mtt) REVERT: D 359 LYS cc_start: 0.5545 (mptt) cc_final: 0.4341 (ptmt) outliers start: 39 outliers final: 21 residues processed: 228 average time/residue: 0.2299 time to fit residues: 75.4628 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 : 1.175 ------------------------------------------------------------------------------- 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: 0.8980 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** D 291 HIS E 58 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.194204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.166452 restraints weight = 15494.921| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.00 r_work: 0.3981 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11986 Z= 0.235 Angle : 0.699 7.717 16266 Z= 0.370 Chirality : 0.050 0.185 1785 Planarity : 0.005 0.066 2070 Dihedral : 12.036 73.851 1827 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.77 % Allowed : 16.60 % Favored : 79.63 % 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: 0.04 (0.21), residues: 1440 helix: 0.37 (0.19), residues: 696 sheet: 0.18 (0.37), residues: 186 loop : -0.27 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 329 HIS 0.008 0.002 HIS D 124 PHE 0.020 0.003 PHE A 357 TYR 0.020 0.002 TYR D 224 ARG 0.006 0.001 ARG C 322 Details of bonding type rmsd hydrogen bonds : bond 0.06198 ( 516) hydrogen bonds : angle 5.74318 ( 1494) covalent geometry : bond 0.00538 (11986) covalent geometry : angle 0.69907 (16266) *********************** 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 226 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4254 (OUTLIER) cc_final: 0.3695 (m90) REVERT: B 47 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.4718 (mpt) REVERT: B 138 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6448 (tm-30) REVERT: B 246 MET cc_start: 0.7993 (mmt) cc_final: 0.7607 (mmp) REVERT: B 328 SER cc_start: 0.7482 (t) cc_final: 0.7194 (p) REVERT: B 344 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6165 (tp30) REVERT: C 313 ASP cc_start: 0.7829 (p0) cc_final: 0.5965 (t0) REVERT: D 41 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7273 (t0) REVERT: D 176 LYS cc_start: 0.7194 (tttt) cc_final: 0.6653 (tptp) REVERT: D 186 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7459 (mtt) REVERT: D 291 HIS cc_start: 0.6379 (OUTLIER) cc_final: 0.6056 (t-170) REVERT: D 359 LYS cc_start: 0.5709 (mptt) cc_final: 0.4332 (ptmt) REVERT: E 102 ASP cc_start: 0.4528 (m-30) cc_final: 0.3744 (t0) REVERT: E 151 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7398 (tp) outliers start: 47 outliers final: 27 residues processed: 213 average time/residue: 0.2436 time to fit residues: 76.4252 Evaluate side-chains 197 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 239 THR Chi-restraints excluded: chain A residue 287 VAL 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 202 LYS 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 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 D residue 329 TRP 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: 0.0270 chunk 13 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 108 optimal weight: 0.0070 chunk 60 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 0.0570 overall best weight: 0.2974 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.201548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.174372 restraints weight = 15234.776| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.98 r_work: 0.4067 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11986 Z= 0.118 Angle : 0.559 6.811 16266 Z= 0.291 Chirality : 0.044 0.181 1785 Planarity : 0.005 0.056 2070 Dihedral : 10.387 71.466 1825 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.45 % Allowed : 18.04 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.19), residues: 699 sheet: 0.30 (0.38), residues: 182 loop : -0.03 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 203 HIS 0.005 0.001 HIS A 124 PHE 0.021 0.001 PHE A 357 TYR 0.017 0.001 TYR A 224 ARG 0.006 0.000 ARG C 322 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 516) hydrogen bonds : angle 5.23014 ( 1494) covalent geometry : bond 0.00246 (11986) covalent geometry : angle 0.55873 (16266) *********************** 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: 43 poor density : 177 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4257 (OUTLIER) cc_final: 0.3760 (m90) REVERT: B 43 MET cc_start: 0.7291 (tmm) cc_final: 0.6670 (tmm) REVERT: B 47 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.4202 (mpt) REVERT: B 145 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7133 (mm) REVERT: B 246 MET cc_start: 0.7898 (mmt) cc_final: 0.7680 (mmp) REVERT: B 328 SER cc_start: 0.7469 (t) cc_final: 0.7229 (p) REVERT: B 344 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5913 (tp30) REVERT: C 116 ASP cc_start: 0.7441 (m-30) cc_final: 0.7235 (m-30) REVERT: C 313 ASP cc_start: 0.7716 (p0) cc_final: 0.5808 (t0) REVERT: D 41 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7231 (t0) REVERT: D 145 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7364 (mt) REVERT: D 176 LYS cc_start: 0.6983 (tttt) cc_final: 0.6422 (tptp) REVERT: D 186 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7300 (mtt) REVERT: E 102 ASP cc_start: 0.4764 (m-30) cc_final: 0.3903 (t0) REVERT: E 151 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7349 (tp) outliers start: 43 outliers final: 19 residues processed: 203 average time/residue: 0.2621 time to fit residues: 77.6434 Evaluate side-chains 190 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 4.466 ------------------------------------------------------------------------------- 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 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 278 THR 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 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: 1.9990 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.193655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.168239 restraints weight = 15034.189| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.84 r_work: 0.4026 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3927 r_free = 0.3927 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 = 0.3928 r_free = 0.3928 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11986 Z= 0.170 Angle : 0.595 6.648 16266 Z= 0.311 Chirality : 0.045 0.246 1785 Planarity : 0.005 0.056 2070 Dihedral : 9.939 72.622 1825 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.21 % Allowed : 17.88 % 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: 0.31 (0.22), residues: 1440 helix: 0.55 (0.19), residues: 700 sheet: 0.29 (0.38), residues: 188 loop : -0.08 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 329 HIS 0.008 0.001 HIS A 124 PHE 0.016 0.002 PHE A 120 TYR 0.020 0.002 TYR D 224 ARG 0.005 0.000 ARG B 299 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 516) hydrogen bonds : angle 5.31257 ( 1494) covalent geometry : bond 0.00389 (11986) covalent geometry : angle 0.59479 (16266) *********************** 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 214 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4294 (OUTLIER) cc_final: 0.3779 (m90) REVERT: A 234 TYR cc_start: 0.8141 (m-80) cc_final: 0.7833 (m-80) REVERT: B 47 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.4308 (mpt) REVERT: B 145 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7179 (mm) REVERT: B 246 MET cc_start: 0.7940 (mmt) cc_final: 0.7658 (mmp) REVERT: B 300 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6759 (t0) REVERT: B 328 SER cc_start: 0.7483 (t) cc_final: 0.7237 (p) REVERT: B 344 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5825 (tp30) REVERT: C 116 ASP cc_start: 0.7537 (m-30) cc_final: 0.7261 (m-30) REVERT: C 313 ASP cc_start: 0.7841 (p0) cc_final: 0.5857 (t0) REVERT: D 41 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7303 (t0) REVERT: D 145 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7434 (mt) REVERT: D 176 LYS cc_start: 0.7063 (tttt) cc_final: 0.6554 (tptp) REVERT: D 186 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7330 (mtt) REVERT: E 102 ASP cc_start: 0.4588 (m-30) cc_final: 0.3749 (t0) REVERT: E 151 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7321 (tp) outliers start: 40 outliers final: 24 residues processed: 200 average time/residue: 0.3031 time to fit residues: 89.0837 Evaluate side-chains 194 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 186 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 214 LEU 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 A residue 357 PHE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 55 THR 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 278 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN 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 291 HIS 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: 0.8980 chunk 59 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.199358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.172070 restraints weight = 15405.823| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 1.99 r_work: 0.4042 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- 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 = 0.64 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: 0.7331 moved from start: 0.3837 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= 0.132 Angle : 0.553 6.466 16266 Z= 0.288 Chirality : 0.043 0.179 1785 Planarity : 0.004 0.052 2070 Dihedral : 9.341 71.708 1823 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.89 % Allowed : 18.44 % Favored : 78.67 % 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: 0.37 (0.22), residues: 1440 helix: 0.61 (0.19), residues: 700 sheet: 0.30 (0.39), residues: 182 loop : -0.04 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 329 HIS 0.004 0.001 HIS E 105 PHE 0.014 0.001 PHE A 120 TYR 0.019 0.001 TYR D 224 ARG 0.005 0.000 ARG B 299 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 516) hydrogen bonds : angle 5.17436 ( 1494) covalent geometry : bond 0.00293 (11986) covalent geometry : angle 0.55256 (16266) *********************** 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 205 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6683 (mmt) cc_final: 0.6277 (mmm) REVERT: A 155 HIS cc_start: 0.4301 (OUTLIER) cc_final: 0.3744 (m90) REVERT: A 234 TYR cc_start: 0.8159 (m-80) cc_final: 0.7861 (m-80) REVERT: B 47 MET cc_start: 0.6519 (OUTLIER) cc_final: 0.4120 (mpt) REVERT: B 145 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7151 (mm) REVERT: B 246 MET cc_start: 0.7917 (mmt) cc_final: 0.7645 (mmp) REVERT: B 300 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6752 (t0) REVERT: B 328 SER cc_start: 0.7476 (t) cc_final: 0.7233 (p) REVERT: B 344 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5734 (tp30) REVERT: C 116 ASP cc_start: 0.7470 (m-30) cc_final: 0.7209 (m-30) REVERT: C 313 ASP cc_start: 0.7800 (p0) cc_final: 0.5817 (t0) REVERT: D 41 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7246 (t0) REVERT: D 145 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7393 (mt) REVERT: D 176 LYS cc_start: 0.6996 (tttt) cc_final: 0.6311 (tptt) REVERT: D 186 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7229 (mtt) REVERT: E 102 ASP cc_start: 0.4751 (m-30) cc_final: 0.3823 (t0) REVERT: E 151 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7369 (tp) outliers start: 36 outliers final: 22 residues processed: 192 average time/residue: 0.2311 time to fit residues: 65.1358 Evaluate side-chains 191 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 186 MET 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 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN 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 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 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 107 GLN 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: 0.9980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.199019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.171847 restraints weight = 15484.835| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.99 r_work: 0.4040 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11986 Z= 0.139 Angle : 0.558 8.316 16266 Z= 0.292 Chirality : 0.044 0.154 1785 Planarity : 0.004 0.051 2070 Dihedral : 9.090 71.627 1823 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.29 % Allowed : 18.36 % 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: 0.40 (0.22), residues: 1440 helix: 0.64 (0.19), residues: 700 sheet: 0.33 (0.39), residues: 182 loop : -0.04 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 203 HIS 0.004 0.001 HIS D 124 PHE 0.014 0.001 PHE A 120 TYR 0.024 0.001 TYR D 224 ARG 0.004 0.000 ARG B 299 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 516) hydrogen bonds : angle 5.13957 ( 1494) covalent geometry : bond 0.00311 (11986) covalent geometry : angle 0.55846 (16266) *********************** 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 207 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: A 114 MET cc_start: 0.6613 (mmt) cc_final: 0.6324 (mmm) REVERT: A 155 HIS cc_start: 0.4302 (OUTLIER) cc_final: 0.3776 (m90) REVERT: A 234 TYR cc_start: 0.8134 (m-80) cc_final: 0.7872 (m-80) REVERT: B 47 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.3994 (mpt) REVERT: B 138 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6633 (pt0) REVERT: B 246 MET cc_start: 0.7921 (mmt) cc_final: 0.7638 (mmp) REVERT: B 300 ASN cc_start: 0.7350 (OUTLIER) cc_final: 0.6876 (t0) REVERT: B 328 SER cc_start: 0.7502 (t) cc_final: 0.7276 (p) REVERT: B 344 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5747 (tp30) REVERT: C 116 ASP cc_start: 0.7475 (m-30) cc_final: 0.7205 (m-30) REVERT: C 313 ASP cc_start: 0.7834 (p0) cc_final: 0.5866 (t0) REVERT: D 41 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7246 (t0) REVERT: D 145 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7437 (mt) REVERT: D 176 LYS cc_start: 0.6985 (tttt) cc_final: 0.6397 (tptp) REVERT: D 186 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7217 (mtt) REVERT: E 102 ASP cc_start: 0.4756 (m-30) cc_final: 0.3770 (t0) REVERT: E 151 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7314 (tp) outliers start: 41 outliers final: 25 residues processed: 194 average time/residue: 0.2687 time to fit residues: 77.3585 Evaluate side-chains 193 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 ASP 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 291 HIS Chi-restraints excluded: chain B residue 300 ASN 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 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER 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: 0.6980 chunk 100 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 0.0370 chunk 93 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- 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 D 149 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.191184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166819 restraints weight = 15366.680| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.91 r_work: 0.3926 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11986 Z= 0.124 Angle : 0.549 8.995 16266 Z= 0.286 Chirality : 0.043 0.154 1785 Planarity : 0.004 0.049 2070 Dihedral : 8.863 70.965 1821 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.21 % Allowed : 19.01 % 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: 0.50 (0.22), residues: 1440 helix: 0.73 (0.19), residues: 700 sheet: 0.35 (0.39), residues: 180 loop : -0.02 (0.27), residues: 560 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 0.014 0.001 PHE A 120 TYR 0.027 0.001 TYR D 224 ARG 0.006 0.000 ARG D 299 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 516) hydrogen bonds : angle 5.08028 ( 1494) covalent geometry : bond 0.00272 (11986) covalent geometry : angle 0.54884 (16266) *********************** 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 204 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: A 114 MET cc_start: 0.6527 (mmt) cc_final: 0.6279 (mmm) REVERT: A 155 HIS cc_start: 0.4184 (OUTLIER) cc_final: 0.3660 (m90) REVERT: A 234 TYR cc_start: 0.8155 (m-80) cc_final: 0.7905 (m-80) REVERT: B 47 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.3735 (mpt) REVERT: B 145 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7252 (mm) REVERT: B 246 MET cc_start: 0.7951 (mmt) cc_final: 0.7667 (mmp) REVERT: B 300 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.6789 (t0) REVERT: B 328 SER cc_start: 0.7411 (t) cc_final: 0.7180 (p) REVERT: B 344 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5685 (tp30) REVERT: C 116 ASP cc_start: 0.7373 (m-30) cc_final: 0.7156 (m-30) REVERT: C 313 ASP cc_start: 0.7807 (p0) cc_final: 0.5836 (t0) REVERT: D 41 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7163 (t0) REVERT: D 176 LYS cc_start: 0.6933 (tttt) cc_final: 0.6313 (tptp) REVERT: D 186 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7147 (mtt) REVERT: E 60 HIS cc_start: 0.5674 (OUTLIER) cc_final: 0.4289 (t-90) REVERT: E 102 ASP cc_start: 0.4851 (m-30) cc_final: 0.3799 (t0) REVERT: E 151 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7328 (tp) outliers start: 40 outliers final: 24 residues processed: 194 average time/residue: 0.2225 time to fit residues: 63.5272 Evaluate side-chains 193 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 ASP 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 300 ASN 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 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 D residue 319 SER Chi-restraints excluded: chain E residue 60 HIS 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: 7.9990 chunk 63 optimal weight: 0.0170 chunk 123 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.190602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163552 restraints weight = 15298.747| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.01 r_work: 0.3902 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11986 Z= 0.153 Angle : 0.578 9.450 16266 Z= 0.300 Chirality : 0.044 0.155 1785 Planarity : 0.004 0.053 2070 Dihedral : 8.845 71.446 1819 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.53 % Allowed : 18.85 % Favored : 77.63 % 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: 0.42 (0.22), residues: 1440 helix: 0.66 (0.19), residues: 700 sheet: 0.30 (0.39), residues: 179 loop : -0.04 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 203 HIS 0.005 0.001 HIS D 124 PHE 0.015 0.002 PHE C 153 TYR 0.029 0.002 TYR D 224 ARG 0.004 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 516) hydrogen bonds : angle 5.17030 ( 1494) covalent geometry : bond 0.00348 (11986) covalent geometry : angle 0.57760 (16266) *********************** 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 203 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: A 155 HIS cc_start: 0.4234 (OUTLIER) cc_final: 0.3690 (m90) REVERT: A 234 TYR cc_start: 0.8160 (m-80) cc_final: 0.7934 (m-80) REVERT: A 352 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6802 (mp) REVERT: B 47 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.3768 (mpt) REVERT: B 138 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6261 (pt0) REVERT: B 145 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7189 (mm) REVERT: B 246 MET cc_start: 0.7997 (mmt) cc_final: 0.7678 (mmp) REVERT: B 300 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.6768 (t0) REVERT: B 328 SER cc_start: 0.7428 (t) cc_final: 0.7193 (p) REVERT: B 344 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5733 (tp30) REVERT: C 116 ASP cc_start: 0.7447 (m-30) cc_final: 0.7241 (m-30) REVERT: C 313 ASP cc_start: 0.7906 (p0) cc_final: 0.5942 (t0) REVERT: D 41 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7224 (t0) REVERT: D 163 ARG cc_start: 0.6580 (mtt180) cc_final: 0.5966 (mtt-85) REVERT: D 176 LYS cc_start: 0.6985 (tttt) cc_final: 0.6351 (tptp) REVERT: D 186 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7163 (mtt) REVERT: E 60 HIS cc_start: 0.5723 (OUTLIER) cc_final: 0.4299 (t-90) REVERT: E 102 ASP cc_start: 0.4913 (m-30) cc_final: 0.3915 (t0) REVERT: E 128 MET cc_start: 0.2691 (tmm) cc_final: 0.2376 (mmp) outliers start: 44 outliers final: 27 residues processed: 193 average time/residue: 0.2242 time to fit residues: 64.1217 Evaluate side-chains 193 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 ASP 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 A residue 352 LEU 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 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN 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 209 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 138 GLU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 278 THR 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 29 VAL 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 53 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.190478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.163708 restraints weight = 15280.001| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.97 r_work: 0.3910 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11986 Z= 0.131 Angle : 0.566 10.101 16266 Z= 0.294 Chirality : 0.044 0.163 1785 Planarity : 0.004 0.054 2070 Dihedral : 8.761 70.633 1819 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.89 % Allowed : 19.73 % 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: 0.46 (0.22), residues: 1440 helix: 0.69 (0.20), residues: 700 sheet: 0.32 (0.39), residues: 179 loop : -0.02 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 203 HIS 0.004 0.001 HIS D 124 PHE 0.014 0.001 PHE A 120 TYR 0.031 0.001 TYR D 224 ARG 0.004 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 516) hydrogen bonds : angle 5.13988 ( 1494) covalent geometry : bond 0.00293 (11986) covalent geometry : angle 0.56581 (16266) ********************** 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 197 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: A 114 MET cc_start: 0.6559 (mmt) cc_final: 0.6349 (mmm) REVERT: A 155 HIS cc_start: 0.4191 (OUTLIER) cc_final: 0.3655 (m90) REVERT: A 234 TYR cc_start: 0.8184 (m-80) cc_final: 0.7951 (m-80) REVERT: A 352 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6804 (mp) REVERT: B 47 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.3568 (mpt) REVERT: B 138 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6335 (pt0) REVERT: B 145 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7215 (mm) REVERT: B 199 GLN cc_start: 0.7855 (mt0) cc_final: 0.7621 (mp10) REVERT: B 246 MET cc_start: 0.7955 (mmt) cc_final: 0.7752 (mmp) REVERT: B 299 ARG cc_start: 0.6854 (ttp-170) cc_final: 0.6651 (ptt180) REVERT: B 300 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6793 (t0) REVERT: B 328 SER cc_start: 0.7367 (t) cc_final: 0.7142 (p) REVERT: B 344 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5725 (tp30) REVERT: C 116 ASP cc_start: 0.7385 (m-30) cc_final: 0.7165 (m-30) REVERT: C 313 ASP cc_start: 0.7867 (p0) cc_final: 0.5860 (t0) REVERT: D 41 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7183 (t0) REVERT: D 176 LYS cc_start: 0.6940 (tttt) cc_final: 0.6302 (tptp) REVERT: D 186 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7138 (mtt) REVERT: E 60 HIS cc_start: 0.5750 (OUTLIER) cc_final: 0.4202 (t-90) REVERT: E 102 ASP cc_start: 0.4897 (m-30) cc_final: 0.3839 (t0) REVERT: E 128 MET cc_start: 0.2848 (tmm) cc_final: 0.2400 (mmp) outliers start: 36 outliers final: 23 residues processed: 188 average time/residue: 0.2288 time to fit residues: 63.2406 Evaluate side-chains 192 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 ASP 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 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 352 LEU 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 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN 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 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 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 D residue 319 SER 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: 3.9990 chunk 62 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 86 optimal weight: 0.0050 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.0056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN D 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.190798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.163766 restraints weight = 15257.003| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.01 r_work: 0.3905 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 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 = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11986 Z= 0.145 Angle : 0.573 9.105 16266 Z= 0.300 Chirality : 0.044 0.158 1785 Planarity : 0.004 0.051 2070 Dihedral : 8.769 70.778 1819 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.97 % Allowed : 19.97 % Favored : 77.06 % 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: 0.40 (0.22), residues: 1440 helix: 0.66 (0.19), residues: 700 sheet: 0.24 (0.39), residues: 179 loop : -0.04 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 203 HIS 0.005 0.001 HIS D 124 PHE 0.015 0.001 PHE C 153 TYR 0.030 0.001 TYR D 224 ARG 0.003 0.000 ARG B 299 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 516) hydrogen bonds : angle 5.14614 ( 1494) covalent geometry : bond 0.00330 (11986) covalent geometry : angle 0.57320 (16266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7122.07 seconds wall clock time: 126 minutes 38.27 seconds (7598.27 seconds total)