Starting phenix.real_space_refine on Wed Jun 3 14:42:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kaf_62207/06_2026/9kaf_62207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kaf_62207/06_2026/9kaf_62207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kaf_62207/06_2026/9kaf_62207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kaf_62207/06_2026/9kaf_62207.map" model { file = "/net/cci-nas-00/data/ceres_data/9kaf_62207/06_2026/9kaf_62207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kaf_62207/06_2026/9kaf_62207.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.060 sd= 0.745 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4166 2.51 5 N 1097 2.21 5 O 1298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6583 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1603 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 198} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2474 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 319} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2506 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 319} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.59, per 1000 atoms: 0.24 Number of scatterers: 6583 At special positions: 0 Unit cell: (90.75, 96, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1298 8.00 N 1097 7.00 C 4166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 369.4 milliseconds 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1614 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 77.5% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 74 through 97 removed outlier: 3.881A pdb=" N ALA B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 97 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 107 through 124 removed outlier: 3.529A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.743A pdb=" N ARG B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.676A pdb=" N ILE B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 242 Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.662A pdb=" N GLY A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.610A pdb=" N ALA A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 removed outlier: 3.884A pdb=" N LYS A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.652A pdb=" N VAL A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 185 removed outlier: 3.928A pdb=" N GLN A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 199 through 220 Processing helix chain 'A' and resid 223 through 247 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.565A pdb=" N TYR A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 282 removed outlier: 4.142A pdb=" N ILE A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 313 removed outlier: 3.832A pdb=" N PHE A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.645A pdb=" N LYS A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.763A pdb=" N GLN A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.567A pdb=" N GLU A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.571A pdb=" N SER A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 135 through 153 removed outlier: 3.963A pdb=" N VAL C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 184 removed outlier: 3.928A pdb=" N GLN C 162 " --> pdb=" O THR C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 199 through 222 removed outlier: 3.604A pdb=" N SER C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 247 Processing helix chain 'C' and resid 254 through 266 Processing helix chain 'C' and resid 266 through 282 removed outlier: 4.143A pdb=" N ILE C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 313 removed outlier: 3.577A pdb=" N PHE C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 319 Processing helix chain 'C' and resid 323 through 329 removed outlier: 3.646A pdb=" N LYS C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 340 removed outlier: 3.762A pdb=" N GLN C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 removed outlier: 4.226A pdb=" N ARG C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 370 through 390 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 396 through 412 removed outlier: 3.571A pdb=" N SER C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 142 through 147 removed outlier: 5.337A pdb=" N PHE B 170 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N TYR B 146 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 14.293A pdb=" N GLY B 168 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B 167 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER B 188 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP B 169 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 186 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN B 198 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 222 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR B 200 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER B 220 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU B 202 " --> pdb=" O ASP B 218 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 246 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 259 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 253 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU B 271 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU B 144 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 187 through 188 476 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1821 1.33 - 1.45: 946 1.45 - 1.57: 3869 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 6673 Sorted by residual: bond pdb=" CA TYR C 263 " pdb=" C TYR C 263 " ideal model delta sigma weight residual 1.522 1.439 0.083 1.39e-02 5.18e+03 3.53e+01 bond pdb=" CA PHE B 164 " pdb=" C PHE B 164 " ideal model delta sigma weight residual 1.523 1.470 0.054 1.34e-02 5.57e+03 1.60e+01 bond pdb=" CA SER C 145 " pdb=" CB SER C 145 " ideal model delta sigma weight residual 1.530 1.467 0.062 1.56e-02 4.11e+03 1.60e+01 bond pdb=" CA SER A 214 " pdb=" CB SER A 214 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.55e-02 4.16e+03 1.55e+01 bond pdb=" CA SER A 239 " pdb=" CB SER A 239 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.55e-02 4.16e+03 1.51e+01 ... (remaining 6668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 8239 2.37 - 4.73: 657 4.73 - 7.10: 104 7.10 - 9.46: 22 9.46 - 11.83: 7 Bond angle restraints: 9029 Sorted by residual: angle pdb=" N LEU A 197 " pdb=" CA LEU A 197 " pdb=" C LEU A 197 " ideal model delta sigma weight residual 111.71 100.54 11.17 1.15e+00 7.56e-01 9.43e+01 angle pdb=" N VAL A 120 " pdb=" CA VAL A 120 " pdb=" C VAL A 120 " ideal model delta sigma weight residual 111.05 101.57 9.48 1.25e+00 6.40e-01 5.75e+01 angle pdb=" N ILE A 182 " pdb=" CA ILE A 182 " pdb=" C ILE A 182 " ideal model delta sigma weight residual 110.62 101.98 8.64 1.14e+00 7.69e-01 5.75e+01 angle pdb=" N GLN A 196 " pdb=" CA GLN A 196 " pdb=" C GLN A 196 " ideal model delta sigma weight residual 112.93 103.00 9.93 1.33e+00 5.65e-01 5.58e+01 angle pdb=" N SER A 358 " pdb=" CA SER A 358 " pdb=" C SER A 358 " ideal model delta sigma weight residual 111.11 102.18 8.93 1.20e+00 6.94e-01 5.54e+01 ... (remaining 9024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 3671 16.88 - 33.75: 296 33.75 - 50.63: 73 50.63 - 67.51: 21 67.51 - 84.39: 5 Dihedral angle restraints: 4066 sinusoidal: 1578 harmonic: 2488 Sorted by residual: dihedral pdb=" C TYR C 263 " pdb=" N TYR C 263 " pdb=" CA TYR C 263 " pdb=" CB TYR C 263 " ideal model delta harmonic sigma weight residual -122.60 -108.74 -13.86 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C PHE B 164 " pdb=" N PHE B 164 " pdb=" CA PHE B 164 " pdb=" CB PHE B 164 " ideal model delta harmonic sigma weight residual -122.60 -110.10 -12.50 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" CA THR C 266 " pdb=" C THR C 266 " pdb=" N ALA C 267 " pdb=" CA ALA C 267 " ideal model delta harmonic sigma weight residual 180.00 -158.88 -21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 4063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 730 0.064 - 0.129: 224 0.129 - 0.193: 73 0.193 - 0.258: 36 0.258 - 0.322: 13 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CA GLN C 196 " pdb=" N GLN C 196 " pdb=" C GLN C 196 " pdb=" CB GLN C 196 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA VAL A 202 " pdb=" N VAL A 202 " pdb=" C VAL A 202 " pdb=" CB VAL A 202 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1073 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 172 " 0.026 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C HIS C 172 " -0.089 2.00e-02 2.50e+03 pdb=" O HIS C 172 " 0.033 2.00e-02 2.50e+03 pdb=" N THR C 173 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 342 " -0.022 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C GLU C 342 " 0.073 2.00e-02 2.50e+03 pdb=" O GLU C 342 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO C 343 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 253 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C ILE A 253 " -0.073 2.00e-02 2.50e+03 pdb=" O ILE A 253 " 0.027 2.00e-02 2.50e+03 pdb=" N THR A 254 " 0.024 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1940 2.79 - 3.32: 7154 3.32 - 3.85: 10754 3.85 - 4.37: 12359 4.37 - 4.90: 20206 Nonbonded interactions: 52413 Sorted by model distance: nonbonded pdb=" OG SER A 185 " pdb=" N ARG C 201 " model vdw 2.268 3.120 nonbonded pdb=" O PHE C 209 " pdb=" N ALA C 212 " model vdw 2.269 3.120 nonbonded pdb=" O LEU B 161 " pdb=" N ASP B 163 " model vdw 2.289 3.120 nonbonded pdb=" N ASP A 256 " pdb=" OD1 ASP A 256 " model vdw 2.291 3.120 nonbonded pdb=" O GLU A 397 " pdb=" OG SER A 400 " model vdw 2.304 3.040 ... (remaining 52408 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 89 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE )) or resid 147 throug \ h 414)) selection = (chain 'C' and ((resid 89 and (name N or name CA or name C or name O or name CB \ )) or resid 90 through 126 or (resid 127 and (name N or name CA or name C or nam \ e O or name CB )) or resid 128 through 134 or (resid 135 and (name N or name CA \ or name C or name O or name CB )) or resid 136 through 187 or (resid 188 through \ 189 and (name N or name CA or name C or name O or name CB )) or resid 190 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 197 through 306 or (resid 307 and (name N or name CA or name C or name O \ or name CB )) or resid 308 through 414)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.920 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.008 0.083 6673 Z= 0.588 Angle : 1.374 11.827 9029 Z= 0.997 Chirality : 0.082 0.322 1076 Planarity : 0.008 0.096 1162 Dihedral : 13.834 84.385 2452 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 1.88 % Allowed : 4.94 % Favored : 93.18 % Rotamer: Outliers : 3.66 % Allowed : 6.05 % Favored : 90.30 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.29), residues: 851 helix: 0.75 (0.22), residues: 562 sheet: -0.41 (0.66), residues: 70 loop : -1.44 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 395 TYR 0.021 0.002 TYR A 198 PHE 0.026 0.002 PHE C 249 TRP 0.019 0.003 TRP A 216 HIS 0.006 0.001 HIS C 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.59 ( 6673) covalent geometry : angle 1.37352 / 1.00 ( 9029) hydrogen bonds : bond 0.20910 / 13.39 ( 476) hydrogen bonds : angle 6.81554 / 4.76 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 MET cc_start: 0.8503 (tpp) cc_final: 0.6921 (tpp) REVERT: B 141 CYS cc_start: 0.6132 (t) cc_final: 0.4743 (t) REVERT: B 145 VAL cc_start: 0.8414 (m) cc_final: 0.7392 (m) REVERT: B 146 TYR cc_start: 0.7120 (t80) cc_final: 0.6702 (t80) REVERT: B 171 PHE cc_start: 0.7254 (m-10) cc_final: 0.6868 (m-10) REVERT: A 197 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7571 (pp) REVERT: A 210 MET cc_start: 0.7887 (mtp) cc_final: 0.7361 (mmm) REVERT: A 213 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8124 (tp40) REVERT: A 251 CYS cc_start: 0.7468 (m) cc_final: 0.6572 (m) REVERT: A 311 PHE cc_start: 0.7132 (m-80) cc_final: 0.6198 (m-10) REVERT: C 210 MET cc_start: 0.7912 (mmp) cc_final: 0.7691 (mmm) outliers start: 26 outliers final: 12 residues processed: 210 average time/residue: 0.1412 time to fit residues: 35.5147 Evaluate side-chains 127 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN B 229 ASN B 232 GLN A 161 HIS A 232 GLN A 367 HIS C 107 ASN C 172 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.037791 restraints weight = 43548.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.039023 restraints weight = 27409.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.039896 restraints weight = 20221.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.040415 restraints weight = 16441.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.040872 restraints weight = 14405.386| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6673 Z= 0.200 Angle : 0.728 12.375 9029 Z= 0.384 Chirality : 0.042 0.160 1076 Planarity : 0.005 0.074 1162 Dihedral : 7.811 59.329 944 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.59 % Allowed : 2.47 % Favored : 96.94 % Rotamer: Outliers : 3.80 % Allowed : 14.35 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.29), residues: 851 helix: 1.55 (0.21), residues: 625 sheet: -0.59 (0.69), residues: 61 loop : -1.02 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 412 TYR 0.020 0.002 TYR C 292 PHE 0.029 0.002 PHE A 129 TRP 0.019 0.002 TRP B 142 HIS 0.011 0.003 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 ( 6673) covalent geometry : angle 0.72822 / 0.38 ( 9029) hydrogen bonds : bond 0.05510 / 3.75 ( 476) hydrogen bonds : angle 4.54917 / 3.16 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 PHE cc_start: 0.8715 (m-10) cc_final: 0.8120 (m-10) REVERT: B 210 LYS cc_start: 0.9360 (mmmt) cc_final: 0.8921 (mmmt) REVERT: B 252 TYR cc_start: 0.8730 (t80) cc_final: 0.8112 (t80) REVERT: A 121 LEU cc_start: 0.9695 (mt) cc_final: 0.9483 (tp) REVERT: A 256 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8754 (p0) REVERT: A 325 ASP cc_start: 0.8876 (p0) cc_final: 0.8553 (p0) REVERT: A 330 ASN cc_start: 0.9263 (t0) cc_final: 0.8605 (t0) REVERT: C 135 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7470 (mpp-170) REVERT: C 140 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9251 (mm) outliers start: 27 outliers final: 12 residues processed: 151 average time/residue: 0.1147 time to fit residues: 21.3291 Evaluate side-chains 118 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 220 ASN A 367 HIS C 313 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.050495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.037818 restraints weight = 42133.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.039067 restraints weight = 26167.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.039918 restraints weight = 19248.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.040467 restraints weight = 15680.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.040913 restraints weight = 13691.942| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6673 Z= 0.143 Angle : 0.687 12.227 9029 Z= 0.352 Chirality : 0.040 0.141 1076 Planarity : 0.006 0.127 1162 Dihedral : 5.823 58.295 923 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.00 % Favored : 97.53 % Rotamer: Outliers : 2.95 % Allowed : 16.60 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.30), residues: 851 helix: 2.07 (0.21), residues: 625 sheet: -0.02 (0.69), residues: 68 loop : -0.85 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 261 TYR 0.024 0.002 TYR A 408 PHE 0.029 0.001 PHE A 129 TRP 0.013 0.002 TRP A 216 HIS 0.008 0.002 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 6673) covalent geometry : angle 0.68735 / 0.35 ( 9029) hydrogen bonds : bond 0.04606 / 3.12 ( 476) hydrogen bonds : angle 4.28787 / 2.95 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8512 (tp) REVERT: B 171 PHE cc_start: 0.8586 (m-10) cc_final: 0.8043 (m-10) REVERT: B 225 ASP cc_start: 0.9318 (m-30) cc_final: 0.9104 (m-30) REVERT: B 268 PHE cc_start: 0.8852 (m-80) cc_final: 0.8514 (m-80) REVERT: A 170 MET cc_start: 0.8572 (mtp) cc_final: 0.8226 (mmm) REVERT: A 325 ASP cc_start: 0.9005 (p0) cc_final: 0.8665 (p0) REVERT: A 330 ASN cc_start: 0.9384 (t0) cc_final: 0.8746 (t0) REVERT: A 346 ARG cc_start: 0.9357 (tpp80) cc_final: 0.9050 (tpp80) REVERT: C 135 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8305 (mpp-170) REVERT: C 140 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9254 (mm) REVERT: C 313 GLN cc_start: 0.8318 (tt0) cc_final: 0.7423 (tm-30) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 0.1055 time to fit residues: 18.1398 Evaluate side-chains 102 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS A 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.050162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.037437 restraints weight = 42277.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.038678 restraints weight = 26178.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.039545 restraints weight = 19162.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.040142 restraints weight = 15499.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.040468 restraints weight = 13392.355| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6673 Z= 0.132 Angle : 0.659 11.507 9029 Z= 0.337 Chirality : 0.040 0.163 1076 Planarity : 0.004 0.057 1162 Dihedral : 5.279 55.755 921 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.59 % Favored : 96.94 % Rotamer: Outliers : 2.39 % Allowed : 19.13 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.30), residues: 851 helix: 2.15 (0.21), residues: 626 sheet: 0.39 (0.70), residues: 68 loop : -0.82 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 395 TYR 0.023 0.002 TYR A 408 PHE 0.015 0.001 PHE C 353 TRP 0.008 0.001 TRP A 216 HIS 0.010 0.002 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 6673) covalent geometry : angle 0.65893 / 0.34 ( 9029) hydrogen bonds : bond 0.04202 / 2.85 ( 476) hydrogen bonds : angle 4.18195 / 2.88 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 HIS cc_start: 0.8990 (m-70) cc_final: 0.8694 (m90) REVERT: B 141 CYS cc_start: 0.8048 (t) cc_final: 0.7013 (t) REVERT: B 167 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8598 (tp) REVERT: B 171 PHE cc_start: 0.8612 (m-10) cc_final: 0.8188 (m-10) REVERT: B 182 VAL cc_start: 0.9374 (t) cc_final: 0.9140 (p) REVERT: B 210 LYS cc_start: 0.9276 (mmmt) cc_final: 0.8576 (mmmt) REVERT: B 225 ASP cc_start: 0.9347 (m-30) cc_final: 0.9095 (p0) REVERT: B 261 ARG cc_start: 0.9118 (mmm-85) cc_final: 0.8622 (mmm-85) REVERT: B 268 PHE cc_start: 0.8848 (m-80) cc_final: 0.8603 (m-80) REVERT: A 346 ARG cc_start: 0.9397 (tpp80) cc_final: 0.9026 (tpp80) REVERT: C 135 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8309 (mpp-170) outliers start: 17 outliers final: 12 residues processed: 117 average time/residue: 0.1053 time to fit residues: 15.7762 Evaluate side-chains 108 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 PHE Chi-restraints excluded: chain C residue 243 LYS Chi-restraints excluded: chain C residue 302 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS A 367 HIS A 404 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.048926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.036165 restraints weight = 43578.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.037402 restraints weight = 27201.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.038252 restraints weight = 20132.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.038759 restraints weight = 16375.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.039202 restraints weight = 14351.215| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6673 Z= 0.152 Angle : 0.684 13.125 9029 Z= 0.344 Chirality : 0.040 0.152 1076 Planarity : 0.004 0.042 1162 Dihedral : 5.062 52.016 919 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.23 % Favored : 97.30 % Rotamer: Outliers : 2.39 % Allowed : 20.11 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.30), residues: 851 helix: 2.26 (0.21), residues: 622 sheet: 0.50 (0.70), residues: 68 loop : -0.86 (0.53), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 395 TYR 0.024 0.002 TYR A 408 PHE 0.037 0.002 PHE A 129 TRP 0.005 0.001 TRP B 247 HIS 0.011 0.002 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6673) covalent geometry : angle 0.68390 / 0.34 ( 9029) hydrogen bonds : bond 0.04527 / 3.07 ( 476) hydrogen bonds : angle 4.14682 / 2.84 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 HIS cc_start: 0.9098 (m-70) cc_final: 0.8683 (m90) REVERT: B 167 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8803 (tp) REVERT: B 171 PHE cc_start: 0.8629 (m-10) cc_final: 0.8175 (m-10) REVERT: B 182 VAL cc_start: 0.9447 (t) cc_final: 0.9175 (p) REVERT: B 225 ASP cc_start: 0.9268 (m-30) cc_final: 0.8969 (t0) REVERT: B 228 MET cc_start: 0.8960 (tmm) cc_final: 0.8646 (tmm) REVERT: B 252 TYR cc_start: 0.8996 (t80) cc_final: 0.8063 (t80) REVERT: B 258 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8319 (tmm160) REVERT: B 261 ARG cc_start: 0.9189 (mmm-85) cc_final: 0.8842 (mmm-85) REVERT: B 268 PHE cc_start: 0.9009 (m-80) cc_final: 0.8743 (m-80) REVERT: A 325 ASP cc_start: 0.8889 (p0) cc_final: 0.8664 (p0) REVERT: A 330 ASN cc_start: 0.9219 (t0) cc_final: 0.8811 (t0) REVERT: A 346 ARG cc_start: 0.9352 (tpp80) cc_final: 0.9013 (tpp80) REVERT: C 135 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8248 (mpp-170) REVERT: C 187 MET cc_start: 0.0959 (ptt) cc_final: 0.0135 (tpp) outliers start: 17 outliers final: 12 residues processed: 111 average time/residue: 0.1017 time to fit residues: 14.5001 Evaluate side-chains 104 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.048801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.035836 restraints weight = 42943.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.037078 restraints weight = 26738.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.037940 restraints weight = 19711.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.038488 restraints weight = 16068.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.038916 restraints weight = 14024.792| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.6669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6673 Z= 0.128 Angle : 0.669 11.137 9029 Z= 0.338 Chirality : 0.040 0.139 1076 Planarity : 0.004 0.038 1162 Dihedral : 5.093 51.339 919 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.59 % Favored : 96.94 % Rotamer: Outliers : 2.25 % Allowed : 22.22 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.30), residues: 851 helix: 2.20 (0.21), residues: 628 sheet: 0.44 (0.68), residues: 68 loop : -0.61 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 368 TYR 0.024 0.002 TYR A 408 PHE 0.024 0.001 PHE A 129 TRP 0.005 0.001 TRP B 247 HIS 0.009 0.002 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 6673) covalent geometry : angle 0.66912 / 0.34 ( 9029) hydrogen bonds : bond 0.04060 / 2.77 ( 476) hydrogen bonds : angle 3.95606 / 2.71 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 HIS cc_start: 0.8989 (m-70) cc_final: 0.8515 (m-70) REVERT: B 167 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8734 (tp) REVERT: B 171 PHE cc_start: 0.8433 (m-10) cc_final: 0.8213 (m-10) REVERT: B 182 VAL cc_start: 0.9407 (t) cc_final: 0.9149 (p) REVERT: B 225 ASP cc_start: 0.9204 (m-30) cc_final: 0.8878 (t0) REVERT: B 228 MET cc_start: 0.8866 (tmm) cc_final: 0.8637 (tmm) REVERT: B 229 ASN cc_start: 0.8730 (m110) cc_final: 0.8387 (m110) REVERT: B 258 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8538 (ptp-170) REVERT: B 261 ARG cc_start: 0.9241 (mmm-85) cc_final: 0.8931 (mmm-85) REVERT: B 268 PHE cc_start: 0.9063 (m-80) cc_final: 0.8782 (m-80) REVERT: A 182 ILE cc_start: 0.7902 (mm) cc_final: 0.7685 (mt) REVERT: A 346 ARG cc_start: 0.9280 (tpp80) cc_final: 0.8982 (tpp80) REVERT: C 135 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8206 (mpp-170) REVERT: C 187 MET cc_start: 0.1020 (ptt) cc_final: 0.0346 (tpp) REVERT: C 367 HIS cc_start: 0.8727 (m90) cc_final: 0.8462 (m90) outliers start: 16 outliers final: 11 residues processed: 103 average time/residue: 0.0954 time to fit residues: 13.0088 Evaluate side-chains 107 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 PHE Chi-restraints excluded: chain C residue 311 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 0.0020 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.047956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.035420 restraints weight = 42932.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.036556 restraints weight = 26985.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.037339 restraints weight = 20037.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.037899 restraints weight = 16412.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.038235 restraints weight = 14324.985| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6673 Z= 0.167 Angle : 0.704 12.006 9029 Z= 0.361 Chirality : 0.041 0.195 1076 Planarity : 0.004 0.039 1162 Dihedral : 5.085 49.542 919 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.59 % Favored : 96.94 % Rotamer: Outliers : 2.67 % Allowed : 21.66 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.30), residues: 851 helix: 2.17 (0.21), residues: 622 sheet: 0.32 (0.66), residues: 68 loop : -0.43 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 368 TYR 0.022 0.002 TYR A 408 PHE 0.014 0.001 PHE A 302 TRP 0.004 0.001 TRP B 247 HIS 0.008 0.002 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 ( 6673) covalent geometry : angle 0.70402 / 0.36 ( 9029) hydrogen bonds : bond 0.04898 / 3.34 ( 476) hydrogen bonds : angle 4.18561 / 2.89 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 HIS cc_start: 0.9141 (m-70) cc_final: 0.8716 (m-70) REVERT: B 167 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8992 (tp) REVERT: B 171 PHE cc_start: 0.8634 (m-10) cc_final: 0.8411 (m-10) REVERT: B 182 VAL cc_start: 0.9473 (t) cc_final: 0.9233 (p) REVERT: B 225 ASP cc_start: 0.9240 (m-30) cc_final: 0.8906 (t0) REVERT: B 228 MET cc_start: 0.8914 (tmm) cc_final: 0.8674 (tmm) REVERT: B 229 ASN cc_start: 0.8709 (m110) cc_final: 0.8297 (m110) REVERT: B 252 TYR cc_start: 0.8976 (t80) cc_final: 0.8443 (t80) REVERT: B 258 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8538 (ptp-170) REVERT: B 261 ARG cc_start: 0.9294 (mmm-85) cc_final: 0.8958 (mmm-85) REVERT: B 268 PHE cc_start: 0.9169 (m-80) cc_final: 0.8918 (m-80) REVERT: A 170 MET cc_start: 0.8753 (mmm) cc_final: 0.8122 (tmm) REVERT: A 346 ARG cc_start: 0.9319 (tpp80) cc_final: 0.8803 (tpp80) REVERT: C 135 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8270 (mpp-170) REVERT: C 187 MET cc_start: 0.1285 (ptt) cc_final: 0.0615 (tpp) outliers start: 19 outliers final: 13 residues processed: 110 average time/residue: 0.0836 time to fit residues: 12.2011 Evaluate side-chains 106 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 PHE Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 356 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.049015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.036033 restraints weight = 42858.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.037251 restraints weight = 27016.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.038118 restraints weight = 19970.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.038643 restraints weight = 16275.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.039095 restraints weight = 14197.456| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6673 Z= 0.125 Angle : 0.705 11.790 9029 Z= 0.354 Chirality : 0.041 0.194 1076 Planarity : 0.003 0.037 1162 Dihedral : 5.191 50.305 919 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.94 % Favored : 96.83 % Rotamer: Outliers : 1.97 % Allowed : 23.21 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.30), residues: 851 helix: 2.14 (0.21), residues: 630 sheet: 0.45 (0.65), residues: 68 loop : -0.59 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 163 TYR 0.021 0.002 TYR A 408 PHE 0.020 0.001 PHE A 129 TRP 0.007 0.001 TRP B 247 HIS 0.008 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6673) covalent geometry : angle 0.70476 / 0.35 ( 9029) hydrogen bonds : bond 0.03810 / 2.62 ( 476) hydrogen bonds : angle 3.94025 / 2.74 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 HIS cc_start: 0.9034 (m-70) cc_final: 0.8724 (m-70) REVERT: B 167 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8765 (tp) REVERT: B 171 PHE cc_start: 0.8466 (m-10) cc_final: 0.8222 (m-10) REVERT: B 182 VAL cc_start: 0.9399 (t) cc_final: 0.9142 (p) REVERT: B 225 ASP cc_start: 0.9240 (m-30) cc_final: 0.8918 (t0) REVERT: B 228 MET cc_start: 0.8845 (tmm) cc_final: 0.8577 (tmm) REVERT: B 229 ASN cc_start: 0.8561 (m110) cc_final: 0.7955 (m110) REVERT: B 252 TYR cc_start: 0.8892 (t80) cc_final: 0.8393 (t80) REVERT: B 261 ARG cc_start: 0.9258 (mmm-85) cc_final: 0.8943 (mmm-85) REVERT: B 268 PHE cc_start: 0.9173 (m-80) cc_final: 0.8897 (m-80) REVERT: A 170 MET cc_start: 0.8703 (mmm) cc_final: 0.8182 (tmm) REVERT: A 346 ARG cc_start: 0.9267 (tpp80) cc_final: 0.8807 (tpp80) REVERT: C 135 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8167 (mpp-170) REVERT: C 187 MET cc_start: 0.1026 (ptt) cc_final: 0.0229 (tpp) outliers start: 14 outliers final: 12 residues processed: 104 average time/residue: 0.0929 time to fit residues: 12.6922 Evaluate side-chains 104 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 PHE Chi-restraints excluded: chain C residue 311 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.046917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.034186 restraints weight = 44956.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.035379 restraints weight = 27727.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.036192 restraints weight = 20401.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.036704 restraints weight = 16655.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.037098 restraints weight = 14593.110| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.7409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6673 Z= 0.203 Angle : 0.730 10.762 9029 Z= 0.383 Chirality : 0.042 0.197 1076 Planarity : 0.004 0.068 1162 Dihedral : 5.182 48.161 919 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.53 % Favored : 96.24 % Rotamer: Outliers : 2.11 % Allowed : 22.93 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.30), residues: 851 helix: 2.02 (0.21), residues: 626 sheet: 0.34 (0.65), residues: 68 loop : -0.80 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 111 TYR 0.018 0.002 TYR C 292 PHE 0.023 0.002 PHE A 129 TRP 0.005 0.001 TRP B 247 HIS 0.007 0.002 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 ( 6673) covalent geometry : angle 0.72990 / 0.38 ( 9029) hydrogen bonds : bond 0.05410 / 3.67 ( 476) hydrogen bonds : angle 4.32092 / 3.02 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 HIS cc_start: 0.9192 (m-70) cc_final: 0.8837 (m-70) REVERT: B 167 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9101 (tp) REVERT: B 170 PHE cc_start: 0.8983 (t80) cc_final: 0.8430 (t80) REVERT: B 171 PHE cc_start: 0.8544 (m-10) cc_final: 0.8246 (m-10) REVERT: B 173 MET cc_start: 0.9069 (mmp) cc_final: 0.8394 (mmp) REVERT: B 225 ASP cc_start: 0.9229 (m-30) cc_final: 0.8905 (t0) REVERT: B 228 MET cc_start: 0.8824 (tmm) cc_final: 0.8554 (tmm) REVERT: B 229 ASN cc_start: 0.8637 (m110) cc_final: 0.8027 (m110) REVERT: B 252 TYR cc_start: 0.8790 (t80) cc_final: 0.8180 (t80) REVERT: B 261 ARG cc_start: 0.9269 (mmm-85) cc_final: 0.8960 (mmm-85) REVERT: B 268 PHE cc_start: 0.9199 (m-80) cc_final: 0.8986 (m-80) REVERT: A 170 MET cc_start: 0.8608 (mmm) cc_final: 0.8127 (mmm) REVERT: A 330 ASN cc_start: 0.9142 (t0) cc_final: 0.8875 (t0) REVERT: A 346 ARG cc_start: 0.9269 (tpp80) cc_final: 0.8874 (tpp80) REVERT: A 404 ASN cc_start: 0.9356 (m110) cc_final: 0.9058 (p0) REVERT: A 408 TYR cc_start: 0.9126 (t80) cc_final: 0.8874 (t80) REVERT: C 187 MET cc_start: 0.1335 (ptt) cc_final: 0.0606 (tpp) REVERT: C 317 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8840 (pt0) REVERT: C 367 HIS cc_start: 0.8855 (m90) cc_final: 0.8501 (m90) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.0859 time to fit residues: 11.8515 Evaluate side-chains 95 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 PHE Chi-restraints excluded: chain C residue 317 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 0.0060 chunk 13 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.048566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.035812 restraints weight = 43207.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.037006 restraints weight = 26984.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.037836 restraints weight = 19877.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.038382 restraints weight = 16160.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.038808 restraints weight = 14046.932| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.7550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6673 Z= 0.144 Angle : 0.777 17.139 9029 Z= 0.392 Chirality : 0.042 0.195 1076 Planarity : 0.004 0.082 1162 Dihedral : 5.265 50.765 919 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.06 % Favored : 96.59 % Rotamer: Outliers : 1.83 % Allowed : 23.91 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.30), residues: 851 helix: 1.96 (0.21), residues: 629 sheet: 0.26 (0.64), residues: 69 loop : -0.64 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 143 TYR 0.017 0.002 TYR A 408 PHE 0.024 0.001 PHE A 129 TRP 0.012 0.002 TRP B 142 HIS 0.008 0.002 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6673) covalent geometry : angle 0.77726 / 0.39 ( 9029) hydrogen bonds : bond 0.04312 / 2.96 ( 476) hydrogen bonds : angle 4.20289 / 2.94 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 HIS cc_start: 0.9171 (m-70) cc_final: 0.8789 (m-70) REVERT: B 167 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8940 (tp) REVERT: B 171 PHE cc_start: 0.8191 (m-10) cc_final: 0.7806 (m-10) REVERT: B 173 MET cc_start: 0.9003 (mmp) cc_final: 0.8644 (ppp) REVERT: B 182 VAL cc_start: 0.9413 (m) cc_final: 0.7807 (t) REVERT: B 225 ASP cc_start: 0.9205 (m-30) cc_final: 0.8907 (t0) REVERT: B 228 MET cc_start: 0.8813 (tmm) cc_final: 0.8547 (tmm) REVERT: B 229 ASN cc_start: 0.8504 (m110) cc_final: 0.7864 (m110) REVERT: B 252 TYR cc_start: 0.8772 (t80) cc_final: 0.8185 (t80) REVERT: B 261 ARG cc_start: 0.9251 (mmm-85) cc_final: 0.8944 (mmm-85) REVERT: B 268 PHE cc_start: 0.9203 (m-80) cc_final: 0.8974 (m-80) REVERT: A 111 LYS cc_start: 0.8943 (ptpp) cc_final: 0.8715 (pttm) REVERT: A 170 MET cc_start: 0.8646 (mmm) cc_final: 0.8184 (mmm) REVERT: A 408 TYR cc_start: 0.9136 (t80) cc_final: 0.8909 (t80) REVERT: C 135 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8171 (mpp-170) REVERT: C 170 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8243 (ttp) REVERT: C 187 MET cc_start: 0.1299 (ptt) cc_final: 0.0670 (tpp) REVERT: C 317 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8781 (pt0) REVERT: C 367 HIS cc_start: 0.8835 (m90) cc_final: 0.8472 (m90) outliers start: 13 outliers final: 9 residues processed: 97 average time/residue: 0.1029 time to fit residues: 12.9404 Evaluate side-chains 101 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 PHE Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 317 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.049640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.036542 restraints weight = 43233.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.037734 restraints weight = 27209.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.038622 restraints weight = 20148.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.039171 restraints weight = 16457.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.039589 restraints weight = 14364.107| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.7732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6673 Z= 0.137 Angle : 0.760 16.987 9029 Z= 0.382 Chirality : 0.042 0.184 1076 Planarity : 0.004 0.056 1162 Dihedral : 5.179 49.526 919 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.29 % Favored : 96.36 % Rotamer: Outliers : 1.69 % Allowed : 23.63 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.30), residues: 851 helix: 2.03 (0.21), residues: 624 sheet: 0.35 (0.64), residues: 69 loop : -0.62 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 143 TYR 0.016 0.002 TYR A 408 PHE 0.022 0.001 PHE A 129 TRP 0.013 0.002 TRP B 142 HIS 0.005 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 6673) covalent geometry : angle 0.76017 / 0.38 ( 9029) hydrogen bonds : bond 0.03922 / 2.70 ( 476) hydrogen bonds : angle 4.07298 / 2.86 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1242.13 seconds wall clock time: 22 minutes 20.10 seconds (1340.10 seconds total)