Starting phenix.real_space_refine on Wed Nov 20 03:19:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/11_2024/8d45_27175.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/11_2024/8d45_27175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/11_2024/8d45_27175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/11_2024/8d45_27175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/11_2024/8d45_27175.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d45_27175/11_2024/8d45_27175.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 6716 2.51 5 N 1846 2.21 5 O 1944 1.98 5 H 10370 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20932 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5225 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 bond proxies already assigned to first conformer: 5239 Chain: "B" Number of atoms: 5225 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 bond proxies already assigned to first conformer: 5239 Chain: "C" Number of atoms: 5225 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 339, 5201 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 316} Chain breaks: 2 bond proxies already assigned to first conformer: 5239 Chain: "D" Number of atoms: 5257 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 5233 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 318} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 341, 5233 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 318} Chain breaks: 2 bond proxies already assigned to first conformer: 5272 Time building chain proxies: 18.31, per 1000 atoms: 0.87 Number of scatterers: 20932 At special positions: 0 Unit cell: (103.79, 63.13, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 1944 8.00 N 1846 7.00 C 6716 6.00 H 10370 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.77 Conformation dependent library (CDL) restraints added in 3.5 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 54.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 52 through 67 Processing helix chain 'A' and resid 96 through 113 removed outlier: 3.752A pdb=" N ASN A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 152 removed outlier: 3.906A pdb=" N VAL A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.700A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 Processing helix chain 'A' and resid 220 through 239 Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.853A pdb=" N ASP A 263 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.739A pdb=" N ARG A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 332 through 338 removed outlier: 4.006A pdb=" N MET A 337 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 96 through 112 Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.871A pdb=" N VAL B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 148 " --> pdb=" O GLN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 3.535A pdb=" N ALA B 167 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 209 Processing helix chain 'B' and resid 222 through 239 Processing helix chain 'B' and resid 277 through 292 removed outlier: 4.011A pdb=" N ARG B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.959A pdb=" N MET B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 348 through 355 removed outlier: 3.515A pdb=" N TRP B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 19 Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.708A pdb=" N GLU C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 96 through 113 removed outlier: 3.644A pdb=" N ASN C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 152 removed outlier: 3.902A pdb=" N VAL C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 3.659A pdb=" N ALA C 167 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 209 Processing helix chain 'C' and resid 222 through 238 Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.000A pdb=" N ARG C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 322 through 328 Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.536A pdb=" N ASP C 336 " --> pdb=" O SER C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 348 through 355 removed outlier: 3.574A pdb=" N TRP C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 28 through 33 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 52 through 67 Processing helix chain 'D' and resid 96 through 112 Processing helix chain 'D' and resid 134 through 152 removed outlier: 3.871A pdb=" N VAL D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 148 " --> pdb=" O GLN D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 176 removed outlier: 3.557A pdb=" N ALA D 167 " --> pdb=" O HIS D 163 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 220 through 238 Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.845A pdb=" N ILE D 262 " --> pdb=" O GLN D 259 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP D 263 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 4.009A pdb=" N ARG D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Proline residue: D 316 - end of helix Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.922A pdb=" N MET D 337 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 348 through 355 removed outlier: 3.697A pdb=" N TRP D 352 " --> pdb=" O ARG D 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 123 removed outlier: 5.833A pdb=" N VAL A 122 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 72 removed outlier: 3.569A pdb=" N ALA B 119 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 244 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 70 through 72 removed outlier: 6.619A pdb=" N LEU C 156 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR C 184 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA C 158 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 70 through 72 518 hydrogen bonds defined for protein. 1440 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: 8.82 Time building geometry restraints manager: 6.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 10342 1.02 - 1.22: 33 1.22 - 1.42: 4492 1.42 - 1.61: 6246 1.61 - 1.81: 84 Bond restraints: 21197 Sorted by residual: bond pdb=" NE ARG B 108 " pdb=" HE ARG B 108 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C TRP B 44 " pdb=" N THR B 45 " ideal model delta sigma weight residual 1.331 1.384 -0.053 2.07e-02 2.33e+03 6.62e+00 bond pdb=" C TRP C 44 " pdb=" N THR C 45 " ideal model delta sigma weight residual 1.331 1.378 -0.047 2.07e-02 2.33e+03 5.09e+00 bond pdb=" N THR B 222 " pdb=" CA THR B 222 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.25e-02 6.40e+03 4.23e+00 bond pdb=" N THR C 222 " pdb=" CA THR C 222 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.27e-02 6.20e+03 3.26e+00 ... (remaining 21192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 36595 1.47 - 2.94: 1590 2.94 - 4.41: 173 4.41 - 5.88: 31 5.88 - 7.35: 3 Bond angle restraints: 38392 Sorted by residual: angle pdb=" CG LYS A 139 " pdb=" CD LYS A 139 " pdb=" CE LYS A 139 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" N ASN A 152 " pdb=" CA ASN A 152 " pdb=" C ASN A 152 " ideal model delta sigma weight residual 110.91 107.56 3.35 1.17e+00 7.31e-01 8.18e+00 angle pdb=" N ARG A 239 " pdb=" CA ARG A 239 " pdb=" C ARG A 239 " ideal model delta sigma weight residual 111.24 107.32 3.92 1.38e+00 5.25e-01 8.09e+00 angle pdb=" N ARG B 239 " pdb=" CA ARG B 239 " pdb=" C ARG B 239 " ideal model delta sigma weight residual 111.24 107.40 3.84 1.38e+00 5.25e-01 7.74e+00 angle pdb=" N ASN C 152 " pdb=" CA ASN C 152 " pdb=" C ASN C 152 " ideal model delta sigma weight residual 110.91 107.68 3.23 1.17e+00 7.31e-01 7.63e+00 ... (remaining 38387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 8644 17.62 - 35.24: 929 35.24 - 52.87: 323 52.87 - 70.49: 83 70.49 - 88.11: 27 Dihedral angle restraints: 10006 sinusoidal: 5439 harmonic: 4567 Sorted by residual: dihedral pdb=" CA ASP C 336 " pdb=" C ASP C 336 " pdb=" N MET C 337 " pdb=" CA MET C 337 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE C 74 " pdb=" C PHE C 74 " pdb=" N THR C 75 " pdb=" CA THR C 75 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE D 74 " pdb=" C PHE D 74 " pdb=" N THR D 75 " pdb=" CA THR D 75 " ideal model delta harmonic sigma weight residual 180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 10003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 853 0.029 - 0.058: 422 0.058 - 0.087: 176 0.087 - 0.115: 80 0.115 - 0.144: 23 Chirality restraints: 1554 Sorted by residual: chirality pdb=" CA PRO A 46 " pdb=" N PRO A 46 " pdb=" C PRO A 46 " pdb=" CB PRO A 46 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA PRO B 46 " pdb=" N PRO B 46 " pdb=" C PRO B 46 " pdb=" CB PRO B 46 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL A 196 " pdb=" N VAL A 196 " pdb=" C VAL A 196 " pdb=" CB VAL A 196 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1551 not shown) Planarity restraints: 3201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 109 " -0.077 2.00e-02 2.50e+03 8.49e-02 1.08e+02 pdb=" CD GLN B 109 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN B 109 " 0.077 2.00e-02 2.50e+03 pdb=" NE2 GLN B 109 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN B 109 " 0.125 2.00e-02 2.50e+03 pdb="HE22 GLN B 109 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 315 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO D 316 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 316 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 316 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 315 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO C 316 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 316 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 316 " -0.040 5.00e-02 4.00e+02 ... (remaining 3198 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1588 2.21 - 2.81: 45468 2.81 - 3.41: 62571 3.41 - 4.00: 84710 4.00 - 4.60: 129854 Nonbonded interactions: 324191 Sorted by model distance: nonbonded pdb=" H ALA C 158 " pdb=" O ALA C 182 " model vdw 1.613 2.450 nonbonded pdb=" O ALA C 158 " pdb=" H THR C 184 " model vdw 1.626 2.450 nonbonded pdb=" O ILE D 24 " pdb=" H ASN D 69 " model vdw 1.686 2.450 nonbonded pdb=" O ILE A 357 " pdb="HD22 ASN B 364 " model vdw 1.686 2.450 nonbonded pdb=" O ILE B 24 " pdb=" H ASN B 69 " model vdw 1.700 2.450 ... (remaining 324186 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 9 through 14 or resid 16 through 325 or resid 327 through \ 372)) selection = (chain 'B' and (resid 9 through 14 or resid 16 through 325 or resid 327 through \ 372)) selection = (chain 'C' and (resid 9 through 14 or resid 16 through 325 or resid 327 through \ 372)) selection = (chain 'D' and (resid 9 through 14 or resid 16 through 127 or resid 134 through \ 325 or resid 327 through 372)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.380 Extract box with map and model: 0.810 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 56.690 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.130 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:14.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.004 0.053 10827 Z= 0.288 Angle : 0.788 7.348 14666 Z= 0.445 Chirality : 0.044 0.144 1554 Planarity : 0.007 0.072 1935 Dihedral : 17.508 88.110 4022 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.92 % Allowed : 18.26 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1342 helix: -0.69 (0.19), residues: 676 sheet: -1.97 (0.32), residues: 132 loop : -0.76 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 342 HIS 0.007 0.002 HIS A 306 PHE 0.034 0.003 PHE B 155 TYR 0.016 0.002 TYR C 295 ARG 0.009 0.001 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 1.752 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: C 71 MET cc_start: 0.7725 (mmt) cc_final: 0.7139 (mmt) outliers start: 8 outliers final: 7 residues processed: 145 average time/residue: 1.9261 time to fit residues: 309.4197 Evaluate side-chains 138 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 186 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 290 ASN B 152 ASN B 290 ASN C 152 ASN C 354 ASN D 152 ASN D 290 ASN D 354 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10827 Z= 0.324 Angle : 0.678 5.223 14666 Z= 0.357 Chirality : 0.043 0.151 1554 Planarity : 0.007 0.061 1935 Dihedral : 5.198 42.046 1483 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.48 % Allowed : 16.51 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.22), residues: 1342 helix: -0.54 (0.19), residues: 679 sheet: -2.16 (0.32), residues: 130 loop : -0.75 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 342 HIS 0.008 0.002 HIS D 243 PHE 0.012 0.002 PHE C 141 TYR 0.017 0.002 TYR B 295 ARG 0.006 0.001 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.747 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: A 31 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.5852 (t80) REVERT: B 31 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7110 (t80) REVERT: B 321 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8323 (mp) REVERT: C 31 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6017 (t80) REVERT: C 149 MET cc_start: 0.7350 (mmm) cc_final: 0.7058 (mmp) REVERT: D 31 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6147 (t80) REVERT: D 71 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6295 (mpt) outliers start: 25 outliers final: 8 residues processed: 142 average time/residue: 2.1330 time to fit residues: 334.2133 Evaluate side-chains 137 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 321 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10827 Z= 0.235 Angle : 0.610 4.654 14666 Z= 0.316 Chirality : 0.042 0.139 1554 Planarity : 0.006 0.052 1935 Dihedral : 4.635 27.855 1477 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.66 % Allowed : 16.15 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1342 helix: 0.13 (0.20), residues: 648 sheet: -2.24 (0.33), residues: 138 loop : -0.49 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.006 0.002 HIS C 60 PHE 0.011 0.002 PHE D 141 TYR 0.016 0.002 TYR C 295 ARG 0.003 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.540 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: A 31 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6018 (t80) REVERT: B 31 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7135 (t80) REVERT: B 321 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8305 (mp) REVERT: B 356 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7267 (tpt170) REVERT: C 21 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: C 31 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.6186 (t80) REVERT: C 213 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7112 (mm) REVERT: D 31 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.6553 (t80) outliers start: 27 outliers final: 9 residues processed: 138 average time/residue: 2.1407 time to fit residues: 326.4282 Evaluate side-chains 136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 321 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN B 354 ASN C 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10827 Z= 0.225 Angle : 0.587 4.801 14666 Z= 0.302 Chirality : 0.041 0.138 1554 Planarity : 0.006 0.086 1935 Dihedral : 4.468 26.278 1477 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.29 % Allowed : 16.61 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1342 helix: 0.54 (0.20), residues: 633 sheet: -2.28 (0.33), residues: 138 loop : -0.21 (0.28), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.006 0.001 HIS C 60 PHE 0.011 0.002 PHE C 148 TYR 0.014 0.002 TYR B 295 ARG 0.002 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.722 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: A 31 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.5918 (t80) REVERT: A 337 MET cc_start: 0.5271 (ptp) cc_final: 0.4533 (ptm) REVERT: B 31 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7027 (t80) REVERT: B 356 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7175 (tpt170) REVERT: C 31 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.6149 (t80) REVERT: D 31 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.6684 (t80) REVERT: D 71 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.5811 (mpm) outliers start: 23 outliers final: 10 residues processed: 141 average time/residue: 1.9677 time to fit residues: 308.9129 Evaluate side-chains 136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 321 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN C 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10827 Z= 0.336 Angle : 0.643 5.298 14666 Z= 0.335 Chirality : 0.043 0.165 1554 Planarity : 0.006 0.076 1935 Dihedral : 4.651 26.013 1477 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.12 % Allowed : 16.33 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1342 helix: 0.07 (0.20), residues: 657 sheet: -2.15 (0.34), residues: 133 loop : -0.58 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 279 HIS 0.008 0.002 HIS C 60 PHE 0.029 0.003 PHE A 155 TYR 0.024 0.002 TYR C 295 ARG 0.005 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.698 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: A 31 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6362 (t80) REVERT: A 337 MET cc_start: 0.5230 (ptp) cc_final: 0.4471 (ptm) REVERT: B 31 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.6903 (t80) REVERT: B 149 MET cc_start: 0.7276 (mmm) cc_final: 0.7042 (mmp) REVERT: B 356 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7299 (tpt170) REVERT: C 31 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6441 (t80) REVERT: D 31 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.6733 (t80) REVERT: D 51 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6288 (mt-10) REVERT: D 71 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.5736 (mpm) outliers start: 32 outliers final: 11 residues processed: 145 average time/residue: 2.1644 time to fit residues: 346.1627 Evaluate side-chains 140 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 245 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN C 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10827 Z= 0.296 Angle : 0.624 5.402 14666 Z= 0.323 Chirality : 0.043 0.152 1554 Planarity : 0.006 0.084 1935 Dihedral : 4.596 25.941 1477 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.84 % Allowed : 16.61 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1342 helix: 0.30 (0.20), residues: 635 sheet: -2.25 (0.34), residues: 133 loop : -0.46 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.007 0.002 HIS C 60 PHE 0.034 0.002 PHE A 155 TYR 0.021 0.002 TYR C 295 ARG 0.003 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.767 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: A 31 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.6370 (t80) REVERT: A 337 MET cc_start: 0.5181 (ptp) cc_final: 0.4413 (ptm) REVERT: B 31 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.6889 (t80) REVERT: B 51 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: B 149 MET cc_start: 0.7252 (mmm) cc_final: 0.7028 (mmp) REVERT: B 356 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7271 (tpt170) REVERT: C 31 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.6499 (t80) REVERT: D 31 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.6775 (t80) REVERT: D 71 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.5724 (mpm) REVERT: D 337 MET cc_start: 0.4633 (ppp) cc_final: 0.4334 (ppp) outliers start: 29 outliers final: 12 residues processed: 143 average time/residue: 2.0945 time to fit residues: 335.3437 Evaluate side-chains 138 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 245 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN C 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10827 Z= 0.241 Angle : 0.604 5.721 14666 Z= 0.311 Chirality : 0.042 0.144 1554 Planarity : 0.006 0.082 1935 Dihedral : 4.505 25.714 1477 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.48 % Allowed : 17.06 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1342 helix: 0.52 (0.20), residues: 633 sheet: -2.36 (0.33), residues: 133 loop : -0.32 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.007 0.001 HIS B 194 PHE 0.031 0.002 PHE A 155 TYR 0.018 0.002 TYR B 295 ARG 0.002 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.591 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: A 31 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6351 (t80) REVERT: A 51 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6159 (mt-10) REVERT: A 337 MET cc_start: 0.5166 (ptp) cc_final: 0.4404 (ptm) REVERT: B 30 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8345 (t) REVERT: B 31 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.6869 (t80) REVERT: B 51 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6480 (mt-10) REVERT: B 149 MET cc_start: 0.7210 (mmm) cc_final: 0.6997 (mmp) REVERT: B 356 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7284 (tpt170) REVERT: C 31 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.6431 (t80) REVERT: D 31 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.6801 (t80) REVERT: D 71 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.5731 (mpm) REVERT: D 337 MET cc_start: 0.4638 (ppp) cc_final: 0.4338 (ppp) outliers start: 25 outliers final: 9 residues processed: 134 average time/residue: 2.0806 time to fit residues: 309.1590 Evaluate side-chains 136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 245 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 163 HIS D 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10827 Z= 0.303 Angle : 0.628 6.011 14666 Z= 0.324 Chirality : 0.043 0.157 1554 Planarity : 0.006 0.082 1935 Dihedral : 4.578 25.351 1477 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.75 % Allowed : 16.79 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.23), residues: 1342 helix: 0.37 (0.20), residues: 635 sheet: -2.40 (0.32), residues: 133 loop : -0.43 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 279 HIS 0.008 0.002 HIS C 60 PHE 0.031 0.002 PHE A 155 TYR 0.022 0.002 TYR B 295 ARG 0.004 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.713 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: A 31 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.6382 (t80) REVERT: A 51 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6158 (mt-10) REVERT: A 337 MET cc_start: 0.5093 (ptp) cc_final: 0.4353 (ptm) REVERT: B 31 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.6868 (t80) REVERT: B 51 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6472 (mt-10) REVERT: B 356 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7290 (tpt170) REVERT: C 31 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.6520 (t80) REVERT: D 31 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6757 (t80) REVERT: D 51 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6302 (mt-10) REVERT: D 71 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.5725 (mpm) REVERT: D 337 MET cc_start: 0.4633 (ppp) cc_final: 0.4332 (ppp) outliers start: 28 outliers final: 10 residues processed: 138 average time/residue: 2.0397 time to fit residues: 312.2585 Evaluate side-chains 135 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 245 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS D 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10827 Z= 0.258 Angle : 0.605 6.675 14666 Z= 0.312 Chirality : 0.042 0.146 1554 Planarity : 0.006 0.082 1935 Dihedral : 4.464 25.210 1477 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.29 % Allowed : 17.16 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.23), residues: 1342 helix: 0.60 (0.20), residues: 633 sheet: -2.39 (0.32), residues: 133 loop : -0.35 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.006 0.001 HIS C 60 PHE 0.031 0.002 PHE A 155 TYR 0.018 0.002 TYR B 295 ARG 0.003 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.715 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: A 31 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6398 (t80) REVERT: A 51 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6158 (mt-10) REVERT: A 337 MET cc_start: 0.5120 (ptp) cc_final: 0.4393 (ptm) REVERT: B 30 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8359 (t) REVERT: B 31 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6842 (t80) REVERT: B 51 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: B 356 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7187 (tpt170) REVERT: C 31 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6517 (t80) REVERT: D 31 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.6813 (t80) REVERT: D 71 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.5709 (mpm) REVERT: D 337 MET cc_start: 0.4603 (ppp) cc_final: 0.4288 (ppp) outliers start: 23 outliers final: 8 residues processed: 134 average time/residue: 2.0792 time to fit residues: 309.2358 Evaluate side-chains 134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS D 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10827 Z= 0.253 Angle : 0.606 6.443 14666 Z= 0.311 Chirality : 0.042 0.146 1554 Planarity : 0.006 0.082 1935 Dihedral : 4.438 24.920 1477 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.02 % Allowed : 17.71 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1342 helix: 0.65 (0.20), residues: 633 sheet: -2.38 (0.32), residues: 133 loop : -0.30 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 279 HIS 0.006 0.002 HIS C 60 PHE 0.031 0.002 PHE A 155 TYR 0.018 0.002 TYR B 295 ARG 0.003 0.000 ARG B 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.527 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: A 31 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6393 (t80) REVERT: A 51 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6144 (mt-10) REVERT: A 337 MET cc_start: 0.5163 (ptp) cc_final: 0.4415 (ptm) REVERT: B 31 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.6841 (t80) REVERT: B 337 MET cc_start: 0.4740 (ppp) cc_final: 0.4450 (pp-130) REVERT: B 356 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7210 (tpt170) REVERT: C 31 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6519 (t80) REVERT: C 231 MET cc_start: 0.7317 (mtt) cc_final: 0.7114 (mtt) REVERT: D 31 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.6821 (t80) REVERT: D 71 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.5687 (mpm) REVERT: D 337 MET cc_start: 0.4677 (ppp) cc_final: 0.4373 (ppp) outliers start: 20 outliers final: 7 residues processed: 127 average time/residue: 2.0758 time to fit residues: 292.7118 Evaluate side-chains 128 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS D 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.178705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.139063 restraints weight = 54996.267| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.05 r_work: 0.3668 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10827 Z= 0.279 Angle : 0.617 6.512 14666 Z= 0.319 Chirality : 0.042 0.151 1554 Planarity : 0.006 0.082 1935 Dihedral : 4.456 24.875 1476 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.74 % Allowed : 17.98 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1342 helix: 0.55 (0.20), residues: 635 sheet: -2.38 (0.32), residues: 133 loop : -0.39 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 279 HIS 0.007 0.002 HIS C 60 PHE 0.029 0.002 PHE A 155 TYR 0.021 0.002 TYR B 295 ARG 0.003 0.000 ARG B 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7752.32 seconds wall clock time: 231 minutes 10.40 seconds (13870.40 seconds total)