Starting phenix.real_space_refine on Wed Jun 18 06:37:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d45_27175/06_2025/8d45_27175.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d45_27175/06_2025/8d45_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/cci-nas-00/data/ceres_data/8d45_27175/06_2025/8d45_27175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d45_27175/06_2025/8d45_27175.map" model { file = "/net/cci-nas-00/data/ceres_data/8d45_27175/06_2025/8d45_27175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d45_27175/06_2025/8d45_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-5710/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: 16.69, per 1000 atoms: 0.80 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: 4.89 Conformation dependent library (CDL) restraints added in 2.8 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: 1.52 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: 7.12 Time building geometry restraints manager: 6.03 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: 1.100 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: 0.360 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 51.520 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.560 ------------------------------------------------------------------------------- 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= 0.201 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 Details of bonding type rmsd hydrogen bonds : bond 0.19437 ( 518) hydrogen bonds : angle 7.46816 ( 1440) covalent geometry : bond 0.00427 (10827) covalent geometry : angle 0.78810 (14666) *********************** 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 : 1.557 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: 1.9325 time to fit residues: 310.5164 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 : 1.481 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.179074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138670 restraints weight = 58253.867| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.25 r_work: 0.3664 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 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 = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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= 0.213 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 Details of bonding type rmsd hydrogen bonds : bond 0.05738 ( 518) hydrogen bonds : angle 5.99681 ( 1440) covalent geometry : bond 0.00488 (10827) covalent geometry : angle 0.67841 (14666) *********************** 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 : 1.474 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: 0.7575 (OUTLIER) cc_final: 0.5838 (t80) REVERT: B 31 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7101 (t80) REVERT: B 321 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8290 (mp) REVERT: C 31 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.6015 (t80) REVERT: C 149 MET cc_start: 0.7331 (mmm) cc_final: 0.7040 (mmp) REVERT: D 31 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.6116 (t80) REVERT: D 71 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6174 (mpt) outliers start: 25 outliers final: 8 residues processed: 142 average time/residue: 2.1018 time to fit residues: 329.5779 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 : 2.094 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.179052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138042 restraints weight = 57799.780| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.27 r_work: 0.3644 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10827 Z= 0.205 Angle : 0.653 4.904 14666 Z= 0.341 Chirality : 0.043 0.146 1554 Planarity : 0.006 0.053 1935 Dihedral : 4.799 28.766 1477 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.84 % Allowed : 15.87 % Favored : 81.28 % 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: -1.06 (0.22), residues: 1342 helix: -0.19 (0.19), residues: 651 sheet: -2.26 (0.33), residues: 138 loop : -0.70 (0.27), residues: 553 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 0.012 0.002 PHE D 261 TYR 0.019 0.002 TYR B 295 ARG 0.004 0.001 ARG D 278 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 518) hydrogen bonds : angle 5.73623 ( 1440) covalent geometry : bond 0.00475 (10827) covalent geometry : angle 0.65328 (14666) *********************** 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 156 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.595 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: 0.7688 (OUTLIER) cc_final: 0.5959 (t80) REVERT: B 31 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6966 (t80) REVERT: B 272 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: B 356 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7405 (tpt170) REVERT: C 31 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.6157 (t80) REVERT: D 31 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6620 (t80) outliers start: 29 outliers final: 10 residues processed: 144 average time/residue: 2.2104 time to fit residues: 350.8931 Evaluate side-chains 135 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 272 GLU Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain B residue 356 ARG 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 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 55 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 103 optimal weight: 0.0370 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.9464 ------------------------------------------------------------------------------- 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 C 163 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.179685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139968 restraints weight = 60691.975| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.60 r_work: 0.3642 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10827 Z= 0.158 Angle : 0.605 4.757 14666 Z= 0.312 Chirality : 0.042 0.138 1554 Planarity : 0.006 0.086 1935 Dihedral : 4.595 26.413 1477 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.39 % Allowed : 16.42 % 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: -0.48 (0.23), residues: 1342 helix: 0.33 (0.20), residues: 633 sheet: -2.25 (0.33), residues: 138 loop : -0.36 (0.28), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.006 0.002 HIS C 60 PHE 0.013 0.002 PHE D 261 TYR 0.019 0.002 TYR B 295 ARG 0.003 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 518) hydrogen bonds : angle 5.49677 ( 1440) covalent geometry : bond 0.00367 (10827) covalent geometry : angle 0.60501 (14666) *********************** 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 152 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.677 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: 0.7648 (OUTLIER) cc_final: 0.5931 (t80) REVERT: B 31 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.6911 (t80) REVERT: B 356 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7361 (tpt170) REVERT: C 31 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6170 (t80) REVERT: C 149 MET cc_start: 0.7265 (mmm) cc_final: 0.7042 (mmp) REVERT: D 31 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.6646 (t80) REVERT: D 71 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.5579 (mpm) outliers start: 24 outliers final: 10 residues processed: 140 average time/residue: 2.0041 time to fit residues: 311.0397 Evaluate side-chains 132 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 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 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 154 ASP Chi-restraints excluded: chain D residue 245 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 76 optimal weight: 0.0670 chunk 54 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 112 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.180192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141322 restraints weight = 57274.329| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.02 r_work: 0.3666 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10827 Z= 0.141 Angle : 0.584 4.980 14666 Z= 0.300 Chirality : 0.041 0.140 1554 Planarity : 0.005 0.075 1935 Dihedral : 4.435 26.061 1477 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.66 % Allowed : 16.79 % 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: -0.23 (0.23), residues: 1342 helix: 0.59 (0.20), residues: 633 sheet: -2.33 (0.33), residues: 138 loop : -0.25 (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 0.031 0.002 PHE A 155 TYR 0.015 0.002 TYR B 295 ARG 0.002 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 518) hydrogen bonds : angle 5.35169 ( 1440) covalent geometry : bond 0.00329 (10827) covalent geometry : angle 0.58369 (14666) *********************** 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 154 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.498 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: 0.7729 (OUTLIER) cc_final: 0.6029 (t80) REVERT: A 337 MET cc_start: 0.5190 (ptp) cc_final: 0.4372 (ptm) REVERT: B 31 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.6908 (t80) REVERT: B 284 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.7341 (t80) REVERT: B 356 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7540 (tpt170) REVERT: C 31 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.6150 (t80) REVERT: C 231 MET cc_start: 0.7474 (mtt) cc_final: 0.7249 (mtt) REVERT: D 31 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.6749 (t80) REVERT: D 51 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6433 (mt-10) REVERT: D 71 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.5629 (mpm) REVERT: D 337 MET cc_start: 0.4523 (ppp) cc_final: 0.4195 (ppp) outliers start: 27 outliers final: 7 residues processed: 145 average time/residue: 1.8734 time to fit residues: 302.2269 Evaluate side-chains 139 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 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 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 51 GLU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 134 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.179662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140149 restraints weight = 62533.133| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.84 r_work: 0.3625 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10827 Z= 0.149 Angle : 0.585 5.445 14666 Z= 0.300 Chirality : 0.041 0.141 1554 Planarity : 0.005 0.083 1935 Dihedral : 4.382 25.661 1477 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.84 % Allowed : 16.79 % Favored : 80.37 % 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: -0.14 (0.23), residues: 1342 helix: 0.67 (0.20), residues: 633 sheet: -2.26 (0.34), residues: 133 loop : -0.24 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 279 HIS 0.006 0.001 HIS C 60 PHE 0.032 0.002 PHE A 155 TYR 0.017 0.002 TYR B 295 ARG 0.002 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 518) hydrogen bonds : angle 5.29118 ( 1440) covalent geometry : bond 0.00349 (10827) covalent geometry : angle 0.58510 (14666) *********************** 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 161 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.528 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: 0.7745 (OUTLIER) cc_final: 0.6080 (t80) REVERT: A 337 MET cc_start: 0.5195 (ptp) cc_final: 0.4415 (ptm) REVERT: B 30 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8323 (t) REVERT: B 31 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.6842 (t80) REVERT: B 148 PHE cc_start: 0.7250 (m-80) cc_final: 0.7021 (m-80) REVERT: B 284 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7395 (t80) REVERT: B 356 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7387 (tpt170) REVERT: C 31 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.6376 (t80) REVERT: C 231 MET cc_start: 0.7425 (mtt) cc_final: 0.7201 (mtt) REVERT: D 31 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6772 (t80) REVERT: D 51 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6438 (mt-10) REVERT: D 71 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.5517 (mpm) REVERT: D 337 MET cc_start: 0.4757 (ppp) cc_final: 0.4437 (ppp) outliers start: 29 outliers final: 12 residues processed: 149 average time/residue: 1.8424 time to fit residues: 305.8193 Evaluate side-chains 143 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 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 152 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 61 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.180280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140648 restraints weight = 61017.005| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.65 r_work: 0.3642 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10827 Z= 0.132 Angle : 0.575 5.669 14666 Z= 0.295 Chirality : 0.041 0.139 1554 Planarity : 0.005 0.080 1935 Dihedral : 4.309 25.309 1477 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.29 % Allowed : 17.34 % Favored : 80.37 % 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: 0.01 (0.23), residues: 1342 helix: 0.84 (0.21), residues: 633 sheet: -2.38 (0.33), residues: 138 loop : -0.16 (0.28), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 279 HIS 0.006 0.001 HIS B 194 PHE 0.028 0.002 PHE A 155 TYR 0.014 0.001 TYR B 295 ARG 0.002 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 518) hydrogen bonds : angle 5.23200 ( 1440) covalent geometry : bond 0.00307 (10827) covalent geometry : angle 0.57486 (14666) *********************** 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 148 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.635 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: 0.7733 (OUTLIER) cc_final: 0.6066 (t80) REVERT: A 51 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6253 (mt-10) REVERT: A 337 MET cc_start: 0.5160 (ptp) cc_final: 0.4411 (ptm) REVERT: B 31 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.6848 (t80) REVERT: B 148 PHE cc_start: 0.7229 (m-80) cc_final: 0.6974 (m-80) REVERT: B 284 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7334 (t80) REVERT: B 356 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7378 (tpt170) REVERT: C 31 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.6375 (t80) REVERT: C 231 MET cc_start: 0.7450 (mtt) cc_final: 0.7197 (mtt) REVERT: C 321 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8171 (mp) REVERT: D 31 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.6774 (t80) REVERT: D 51 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6350 (mt-10) REVERT: D 71 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.5456 (mpm) REVERT: D 337 MET cc_start: 0.4862 (ppp) cc_final: 0.4549 (ppp) outliers start: 23 outliers final: 5 residues processed: 137 average time/residue: 1.9419 time to fit residues: 296.4502 Evaluate side-chains 136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 51 GLU 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 C residue 321 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.179974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.140483 restraints weight = 59718.221| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.46 r_work: 0.3641 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10827 Z= 0.142 Angle : 0.578 5.944 14666 Z= 0.296 Chirality : 0.041 0.138 1554 Planarity : 0.005 0.080 1935 Dihedral : 4.262 24.657 1476 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.02 % Allowed : 17.34 % Favored : 80.64 % 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: 0.07 (0.23), residues: 1342 helix: 0.88 (0.21), residues: 633 sheet: -2.35 (0.33), residues: 133 loop : -0.14 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 279 HIS 0.006 0.001 HIS C 60 PHE 0.031 0.002 PHE A 155 TYR 0.016 0.002 TYR B 295 ARG 0.002 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 518) hydrogen bonds : angle 5.20256 ( 1440) covalent geometry : bond 0.00334 (10827) covalent geometry : angle 0.57836 (14666) *********************** 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 140 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.610 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: 0.7732 (OUTLIER) cc_final: 0.6059 (t80) REVERT: A 51 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6191 (mt-10) REVERT: A 337 MET cc_start: 0.5162 (ptp) cc_final: 0.4413 (ptm) REVERT: B 31 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6819 (t80) REVERT: B 148 PHE cc_start: 0.7204 (m-80) cc_final: 0.6910 (m-80) REVERT: B 284 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7363 (t80) REVERT: B 356 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7385 (tpt170) REVERT: C 31 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.6389 (t80) REVERT: C 231 MET cc_start: 0.7423 (mtt) cc_final: 0.7168 (mtt) REVERT: D 31 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6747 (t80) REVERT: D 51 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6393 (mt-10) REVERT: D 71 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.5505 (mpm) REVERT: D 337 MET cc_start: 0.4861 (ppp) cc_final: 0.4524 (ppp) outliers start: 20 outliers final: 7 residues processed: 131 average time/residue: 2.0113 time to fit residues: 292.1444 Evaluate side-chains 135 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 96 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 90 optimal weight: 0.2980 chunk 119 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN B 143 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.181060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.141973 restraints weight = 56473.827| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.22 r_work: 0.3685 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10827 Z= 0.124 Angle : 0.568 6.694 14666 Z= 0.288 Chirality : 0.041 0.139 1554 Planarity : 0.005 0.081 1935 Dihedral : 4.133 24.109 1476 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.74 % Allowed : 17.71 % 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: 0.29 (0.24), residues: 1342 helix: 1.11 (0.21), residues: 633 sheet: -2.37 (0.33), residues: 138 loop : -0.03 (0.28), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 279 HIS 0.005 0.001 HIS C 60 PHE 0.028 0.002 PHE A 155 TYR 0.012 0.001 TYR B 295 ARG 0.002 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 518) hydrogen bonds : angle 5.10448 ( 1440) covalent geometry : bond 0.00290 (10827) covalent geometry : angle 0.56847 (14666) *********************** 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 141 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.504 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: 0.7623 (OUTLIER) cc_final: 0.5939 (t80) REVERT: A 51 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6279 (mt-10) REVERT: A 337 MET cc_start: 0.5162 (ptp) cc_final: 0.4346 (ptm) REVERT: B 31 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6846 (t80) REVERT: B 148 PHE cc_start: 0.7110 (m-80) cc_final: 0.6767 (m-80) REVERT: B 284 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.7268 (t80) REVERT: B 337 MET cc_start: 0.4763 (ppp) cc_final: 0.4467 (pp-130) REVERT: B 356 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7535 (tpt170) REVERT: C 31 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6343 (t80) REVERT: C 231 MET cc_start: 0.7437 (mtt) cc_final: 0.7201 (mtt) REVERT: D 31 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.6708 (t80) REVERT: D 71 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.5514 (mpm) REVERT: D 148 PHE cc_start: 0.7157 (m-80) cc_final: 0.6882 (m-80) REVERT: D 337 MET cc_start: 0.4796 (ppp) cc_final: 0.4446 (ppp) outliers start: 17 outliers final: 4 residues processed: 132 average time/residue: 1.9071 time to fit residues: 279.8685 Evaluate side-chains 129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 51 GLU 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 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 82 optimal weight: 0.0570 chunk 106 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 1 optimal weight: 0.0030 chunk 27 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.2708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** 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 = 0.4266 r_free = 0.4266 target = 0.182598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142845 restraints weight = 59826.939| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.42 r_work: 0.3704 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10827 Z= 0.108 Angle : 0.557 6.467 14666 Z= 0.282 Chirality : 0.041 0.138 1554 Planarity : 0.005 0.079 1935 Dihedral : 3.952 23.753 1475 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.10 % Allowed : 18.90 % Favored : 80.00 % 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 (0.24), residues: 1342 helix: 1.33 (0.21), residues: 634 sheet: -2.44 (0.33), residues: 138 loop : 0.15 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.004 0.001 HIS C 60 PHE 0.028 0.001 PHE A 155 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 518) hydrogen bonds : angle 5.02406 ( 1440) covalent geometry : bond 0.00254 (10827) covalent geometry : angle 0.55653 (14666) ********************** 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 131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.561 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: 0.7526 (OUTLIER) cc_final: 0.5788 (t80) REVERT: B 31 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.6846 (t80) REVERT: B 148 PHE cc_start: 0.6988 (m-80) cc_final: 0.6674 (m-80) REVERT: B 284 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.7167 (t80) REVERT: B 337 MET cc_start: 0.4743 (ppp) cc_final: 0.4458 (pp-130) REVERT: C 31 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.6253 (t80) REVERT: C 148 PHE cc_start: 0.7034 (m-80) cc_final: 0.6740 (m-80) REVERT: C 231 MET cc_start: 0.7405 (mtt) cc_final: 0.7167 (mtt) REVERT: D 31 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.6677 (t80) REVERT: D 51 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6417 (mt-10) REVERT: D 71 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.5547 (mpm) REVERT: D 148 PHE cc_start: 0.7053 (m-80) cc_final: 0.6765 (m-80) REVERT: D 337 MET cc_start: 0.4716 (ppp) cc_final: 0.4378 (ppp) outliers start: 10 outliers final: 1 residues processed: 125 average time/residue: 1.8618 time to fit residues: 260.0471 Evaluate side-chains 127 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 11 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN B 143 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS D 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.181100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141716 restraints weight = 51169.384| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.80 r_work: 0.3706 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10827 Z= 0.142 Angle : 0.576 6.670 14666 Z= 0.293 Chirality : 0.041 0.138 1554 Planarity : 0.005 0.082 1935 Dihedral : 4.058 24.591 1475 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.28 % Allowed : 18.81 % Favored : 79.91 % 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: 0.37 (0.24), residues: 1342 helix: 1.15 (0.21), residues: 634 sheet: -2.40 (0.32), residues: 138 loop : 0.08 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 279 HIS 0.007 0.001 HIS B 60 PHE 0.026 0.002 PHE A 155 TYR 0.016 0.002 TYR B 295 ARG 0.002 0.000 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 518) hydrogen bonds : angle 5.07024 ( 1440) covalent geometry : bond 0.00334 (10827) covalent geometry : angle 0.57643 (14666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18725.73 seconds wall clock time: 316 minutes 28.33 seconds (18988.33 seconds total)