Starting phenix.real_space_refine on Tue Jun 25 20:40:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb5_19026/06_2024/8rb5_19026.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb5_19026/06_2024/8rb5_19026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb5_19026/06_2024/8rb5_19026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb5_19026/06_2024/8rb5_19026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb5_19026/06_2024/8rb5_19026.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb5_19026/06_2024/8rb5_19026.pdb" } resolution = 3.3 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= 0.002 sd= 0.007 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 21 5.16 5 C 2760 2.51 5 N 762 2.21 5 O 807 1.98 5 H 4422 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8772 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "B" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "C" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Time building chain proxies: 4.50, per 1000 atoms: 0.51 Number of scatterers: 8772 At special positions: 0 Unit cell: (143.104, 70.72, 133.12, 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 21 16.00 O 807 8.00 N 762 7.00 C 2760 6.00 H 4422 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 - 3.50 Amino acid : False - 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: 7.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 70.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 180 through 194 removed outlier: 3.618A pdb=" N GLU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.673A pdb=" N LEU A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 242 Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 264 through 282 removed outlier: 3.559A pdb=" N THR A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.688A pdb=" N ARG A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.807A pdb=" N GLU B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.644A pdb=" N LEU B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 264 through 282 removed outlier: 4.044A pdb=" N LEU B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 302 Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.707A pdb=" N TRP B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 333 Processing helix chain 'C' and resid 180 through 194 removed outlier: 3.885A pdb=" N GLU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 208 removed outlier: 3.648A pdb=" N ARG C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 229 through 242 Processing helix chain 'C' and resid 246 through 256 Processing helix chain 'C' and resid 264 through 282 removed outlier: 3.715A pdb=" N LEU C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 302 Processing helix chain 'C' and resid 305 through 318 Processing helix chain 'C' and resid 323 through 333 244 hydrogen bonds defined for protein. 732 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: 2.83 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 4413 1.12 - 1.30: 759 1.30 - 1.47: 1484 1.47 - 1.64: 2164 1.64 - 1.81: 33 Bond restraints: 8853 Sorted by residual: bond pdb=" N TRP B 309 " pdb=" H TRP B 309 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY B 231 " pdb=" H GLY B 231 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LEU A 275 " pdb=" H LEU A 275 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 GLN B 222 " pdb="HE21 GLN B 222 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU B 275 " pdb=" H LEU B 275 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 8848 not shown) Histogram of bond angle deviations from ideal: 96.09 - 103.92: 82 103.92 - 111.76: 9733 111.76 - 119.59: 3395 119.59 - 127.42: 2809 127.42 - 135.26: 64 Bond angle restraints: 16083 Sorted by residual: angle pdb=" CA ASN A 306 " pdb=" CB ASN A 306 " pdb=" CG ASN A 306 " ideal model delta sigma weight residual 112.60 117.31 -4.71 1.00e+00 1.00e+00 2.22e+01 angle pdb=" OD1 ASN A 306 " pdb=" CG ASN A 306 " pdb=" ND2 ASN A 306 " ideal model delta sigma weight residual 122.60 118.01 4.59 1.00e+00 1.00e+00 2.11e+01 angle pdb=" OE1 GLN A 251 " pdb=" CD GLN A 251 " pdb=" NE2 GLN A 251 " ideal model delta sigma weight residual 122.60 118.16 4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" OE1 GLN C 251 " pdb=" CD GLN C 251 " pdb=" NE2 GLN C 251 " ideal model delta sigma weight residual 122.60 118.32 4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" OE1 GLN C 259 " pdb=" CD GLN C 259 " pdb=" NE2 GLN C 259 " ideal model delta sigma weight residual 122.60 118.34 4.26 1.00e+00 1.00e+00 1.81e+01 ... (remaining 16078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3742 17.66 - 35.32: 203 35.32 - 52.98: 84 52.98 - 70.65: 65 70.65 - 88.31: 10 Dihedral angle restraints: 4104 sinusoidal: 2319 harmonic: 1785 Sorted by residual: dihedral pdb=" CA PRO A 322 " pdb=" C PRO A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA GLU B 263 " pdb=" C GLU B 263 " pdb=" N LYS B 264 " pdb=" CA LYS B 264 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA GLU C 263 " pdb=" C GLU C 263 " pdb=" N LYS C 264 " pdb=" CA LYS C 264 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 307 0.049 - 0.099: 203 0.099 - 0.148: 105 0.148 - 0.197: 35 0.197 - 0.246: 13 Chirality restraints: 663 Sorted by residual: chirality pdb=" CA ASN B 306 " pdb=" N ASN B 306 " pdb=" C ASN B 306 " pdb=" CB ASN B 306 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE C 285 " pdb=" N ILE C 285 " pdb=" C ILE C 285 " pdb=" CB ILE C 285 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE A 285 " pdb=" N ILE A 285 " pdb=" C ILE A 285 " pdb=" CB ILE A 285 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 660 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 162 " 0.173 2.00e-02 2.50e+03 7.09e-02 1.51e+02 pdb=" CG TYR A 162 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 162 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR A 162 " -0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR A 162 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR A 162 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 162 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 162 " 0.129 2.00e-02 2.50e+03 pdb=" HD1 TYR A 162 " -0.029 2.00e-02 2.50e+03 pdb=" HD2 TYR A 162 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 TYR A 162 " -0.020 2.00e-02 2.50e+03 pdb=" HE2 TYR A 162 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 271 " 0.026 9.50e-02 1.11e+02 6.40e-02 9.05e+01 pdb=" NE ARG B 271 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 271 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG B 271 " -0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG B 271 " -0.012 2.00e-02 2.50e+03 pdb="HH11 ARG B 271 " -0.011 2.00e-02 2.50e+03 pdb="HH12 ARG B 271 " 0.108 2.00e-02 2.50e+03 pdb="HH21 ARG B 271 " 0.100 2.00e-02 2.50e+03 pdb="HH22 ARG B 271 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 309 " 0.132 2.00e-02 2.50e+03 4.73e-02 8.94e+01 pdb=" CG TRP B 309 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 309 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP B 309 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 309 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP B 309 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 309 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 309 " 0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 309 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP B 309 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP B 309 " -0.087 2.00e-02 2.50e+03 pdb=" HE1 TRP B 309 " 0.034 2.00e-02 2.50e+03 pdb=" HE3 TRP B 309 " -0.035 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 309 " 0.036 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 309 " -0.030 2.00e-02 2.50e+03 pdb=" HH2 TRP B 309 " 0.020 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 602 2.22 - 2.82: 16810 2.82 - 3.41: 23503 3.41 - 4.01: 28977 4.01 - 4.60: 42766 Nonbonded interactions: 112658 Sorted by model distance: nonbonded pdb=" HG SER C 266 " pdb=" OE1 GLU C 335 " model vdw 1.629 1.850 nonbonded pdb=" HG SER B 266 " pdb=" OE1 GLU B 335 " model vdw 1.632 1.850 nonbonded pdb=" HG SER B 229 " pdb=" OE1 GLU B 232 " model vdw 1.633 1.850 nonbonded pdb=" O VAL C 206 " pdb=" HG SER C 209 " model vdw 1.665 1.850 nonbonded pdb=" O VAL B 206 " pdb=" HG SER B 209 " model vdw 1.666 1.850 ... (remaining 112653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.590 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: 0.120 Extract box with map and model: 2.460 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 30.820 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.012 0.068 4431 Z= 0.766 Angle : 1.719 6.912 5988 Z= 1.158 Chirality : 0.082 0.246 663 Planarity : 0.013 0.083 777 Dihedral : 14.627 88.307 1725 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.64 % Allowed : 1.71 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.30), residues: 534 helix: -1.67 (0.21), residues: 363 sheet: None (None), residues: 0 loop : -0.10 (0.44), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.018 TRP B 309 HIS 0.007 0.005 HIS C 219 PHE 0.051 0.015 PHE B 237 TYR 0.152 0.019 TYR A 162 ARG 0.005 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 211 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.4233 (OUTLIER) cc_final: 0.2271 (m-80) REVERT: A 253 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8419 (mtmt) REVERT: A 296 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7852 (tm-30) REVERT: B 179 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 218 MET cc_start: 0.9042 (tpp) cc_final: 0.8518 (tpt) REVERT: B 253 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8409 (mtmm) REVERT: B 272 LEU cc_start: 0.7938 (tp) cc_final: 0.7732 (tt) REVERT: B 299 MET cc_start: 0.8937 (mtp) cc_final: 0.8694 (mpp) REVERT: C 203 LYS cc_start: 0.8570 (mttt) cc_final: 0.8114 (mtpp) REVERT: C 216 ASP cc_start: 0.8537 (m-30) cc_final: 0.8309 (m-30) REVERT: C 222 GLN cc_start: 0.8671 (mt0) cc_final: 0.8377 (mt0) REVERT: C 228 ILE cc_start: 0.8368 (tt) cc_final: 0.8119 (tt) REVERT: C 253 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8282 (ttmm) REVERT: C 256 ARG cc_start: 0.7434 (ttt90) cc_final: 0.6708 (ttm170) outliers start: 3 outliers final: 0 residues processed: 211 average time/residue: 0.5119 time to fit residues: 124.9424 Evaluate side-chains 144 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4431 Z= 0.250 Angle : 0.613 4.135 5988 Z= 0.331 Chirality : 0.036 0.155 663 Planarity : 0.005 0.037 777 Dihedral : 5.731 39.186 593 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.99 % Allowed : 10.68 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.35), residues: 534 helix: 0.10 (0.26), residues: 375 sheet: None (None), residues: 0 loop : 0.44 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 184 HIS 0.002 0.001 HIS A 219 PHE 0.013 0.002 PHE B 181 TYR 0.011 0.002 TYR B 162 ARG 0.005 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.4082 (OUTLIER) cc_final: 0.2563 (m-80) REVERT: A 218 MET cc_start: 0.9034 (tpp) cc_final: 0.8524 (tpt) REVERT: A 253 LYS cc_start: 0.8744 (mtpt) cc_final: 0.8448 (mtmt) REVERT: A 291 ASP cc_start: 0.7912 (p0) cc_final: 0.7612 (p0) REVERT: A 296 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7665 (tm-30) REVERT: B 162 TYR cc_start: 0.4680 (t80) cc_final: 0.1003 (m-10) REVERT: B 203 LYS cc_start: 0.8813 (mttm) cc_final: 0.8512 (mtpp) REVERT: B 256 ARG cc_start: 0.6995 (tpp-160) cc_final: 0.6112 (ttm170) REVERT: C 216 ASP cc_start: 0.8402 (m-30) cc_final: 0.8141 (m-30) REVERT: C 256 ARG cc_start: 0.7404 (ttt90) cc_final: 0.6700 (ttm170) REVERT: C 272 LEU cc_start: 0.8018 (tp) cc_final: 0.7738 (tt) outliers start: 14 outliers final: 11 residues processed: 162 average time/residue: 0.4453 time to fit residues: 85.2333 Evaluate side-chains 151 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 288 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4431 Z= 0.156 Angle : 0.506 3.813 5988 Z= 0.269 Chirality : 0.034 0.141 663 Planarity : 0.005 0.042 777 Dihedral : 4.980 36.146 593 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.56 % Allowed : 13.25 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.35), residues: 534 helix: 0.83 (0.26), residues: 375 sheet: None (None), residues: 0 loop : 0.69 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 184 HIS 0.001 0.001 HIS A 219 PHE 0.009 0.001 PHE C 181 TYR 0.006 0.001 TYR B 162 ARG 0.007 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.3871 (OUTLIER) cc_final: 0.2450 (m-80) REVERT: A 218 MET cc_start: 0.8987 (tpp) cc_final: 0.8420 (tpt) REVERT: A 253 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8398 (tppt) REVERT: A 291 ASP cc_start: 0.7848 (p0) cc_final: 0.7370 (p0) REVERT: B 162 TYR cc_start: 0.4064 (t80) cc_final: 0.0734 (m-80) REVERT: B 256 ARG cc_start: 0.6984 (tpp-160) cc_final: 0.6198 (ttm170) REVERT: B 282 LYS cc_start: 0.9020 (tppt) cc_final: 0.8798 (tppp) REVERT: B 299 MET cc_start: 0.8939 (mtp) cc_final: 0.8716 (mtt) REVERT: C 216 ASP cc_start: 0.8368 (m-30) cc_final: 0.8109 (m-30) REVERT: C 256 ARG cc_start: 0.7379 (ttt90) cc_final: 0.6732 (ttm170) REVERT: C 272 LEU cc_start: 0.8016 (tp) cc_final: 0.7756 (tt) REVERT: C 328 MET cc_start: 0.6751 (tpp) cc_final: 0.6487 (tpt) outliers start: 12 outliers final: 7 residues processed: 153 average time/residue: 0.4084 time to fit residues: 74.6292 Evaluate side-chains 145 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 233 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4431 Z= 0.285 Angle : 0.551 4.187 5988 Z= 0.297 Chirality : 0.036 0.143 663 Planarity : 0.005 0.041 777 Dihedral : 4.851 36.165 593 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.14 % Allowed : 14.53 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.35), residues: 534 helix: 0.95 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.49 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.001 0.001 HIS C 219 PHE 0.015 0.002 PHE B 181 TYR 0.013 0.002 TYR B 162 ARG 0.004 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.3895 (OUTLIER) cc_final: 0.2500 (m-80) REVERT: A 253 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8411 (mmtt) REVERT: A 291 ASP cc_start: 0.7927 (p0) cc_final: 0.7430 (p0) REVERT: B 162 TYR cc_start: 0.4425 (t80) cc_final: 0.1107 (m-10) REVERT: B 256 ARG cc_start: 0.7113 (tpp-160) cc_final: 0.6386 (ttm170) REVERT: B 283 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8083 (tpp80) REVERT: C 194 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7934 (mp0) REVERT: C 216 ASP cc_start: 0.8433 (m-30) cc_final: 0.8174 (m-30) REVERT: C 256 ARG cc_start: 0.7527 (ttt90) cc_final: 0.6832 (ttm170) REVERT: C 272 LEU cc_start: 0.8050 (tp) cc_final: 0.7761 (tt) outliers start: 10 outliers final: 8 residues processed: 144 average time/residue: 0.3879 time to fit residues: 67.4170 Evaluate side-chains 149 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 233 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4431 Z= 0.193 Angle : 0.503 3.948 5988 Z= 0.265 Chirality : 0.034 0.151 663 Planarity : 0.005 0.041 777 Dihedral : 4.582 35.837 593 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.92 % Allowed : 14.96 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.36), residues: 534 helix: 1.09 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.60 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.001 0.001 HIS C 219 PHE 0.011 0.001 PHE C 181 TYR 0.007 0.001 TYR B 162 ARG 0.003 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.3844 (OUTLIER) cc_final: 0.2447 (m-80) REVERT: A 190 GLU cc_start: 0.8551 (tt0) cc_final: 0.8309 (tt0) REVERT: A 253 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8387 (mmtt) REVERT: B 162 TYR cc_start: 0.4284 (t80) cc_final: 0.1114 (m-10) REVERT: B 256 ARG cc_start: 0.7146 (tpp-160) cc_final: 0.6410 (ttm170) REVERT: B 283 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.8055 (tpp80) REVERT: C 162 TYR cc_start: 0.5177 (OUTLIER) cc_final: 0.4293 (p90) REVERT: C 216 ASP cc_start: 0.8388 (m-30) cc_final: 0.8114 (m-30) REVERT: C 256 ARG cc_start: 0.7508 (ttt90) cc_final: 0.6841 (ttm170) REVERT: C 272 LEU cc_start: 0.8051 (tp) cc_final: 0.7817 (mt) REVERT: C 286 PRO cc_start: 0.8251 (Cg_exo) cc_final: 0.7934 (Cg_endo) REVERT: C 306 ASN cc_start: 0.6965 (m-40) cc_final: 0.6415 (p0) outliers start: 9 outliers final: 6 residues processed: 151 average time/residue: 0.3879 time to fit residues: 70.9602 Evaluate side-chains 146 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 233 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN C 239 GLN C 292 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4431 Z= 0.209 Angle : 0.507 3.951 5988 Z= 0.270 Chirality : 0.034 0.143 663 Planarity : 0.005 0.042 777 Dihedral : 4.425 34.739 593 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.71 % Allowed : 16.88 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.36), residues: 534 helix: 1.19 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.60 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.001 0.000 HIS C 219 PHE 0.011 0.001 PHE C 181 TYR 0.007 0.001 TYR B 162 ARG 0.004 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.3890 (OUTLIER) cc_final: 0.2442 (m-80) REVERT: A 190 GLU cc_start: 0.8529 (tt0) cc_final: 0.8302 (tt0) REVERT: A 253 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8393 (tppt) REVERT: B 162 TYR cc_start: 0.4311 (t80) cc_final: 0.1207 (m-10) REVERT: B 256 ARG cc_start: 0.7146 (tpp-160) cc_final: 0.6289 (ttm170) REVERT: B 283 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.8082 (tpp80) REVERT: C 162 TYR cc_start: 0.5167 (OUTLIER) cc_final: 0.4280 (p90) REVERT: C 216 ASP cc_start: 0.8385 (m-30) cc_final: 0.8089 (m-30) REVERT: C 256 ARG cc_start: 0.7551 (ttt90) cc_final: 0.6878 (ttm170) REVERT: C 286 PRO cc_start: 0.8172 (Cg_exo) cc_final: 0.7952 (Cg_endo) REVERT: C 306 ASN cc_start: 0.7028 (m-40) cc_final: 0.6479 (p0) outliers start: 8 outliers final: 6 residues processed: 143 average time/residue: 0.4059 time to fit residues: 69.8903 Evaluate side-chains 141 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 233 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4431 Z= 0.214 Angle : 0.512 4.005 5988 Z= 0.271 Chirality : 0.034 0.145 663 Planarity : 0.005 0.041 777 Dihedral : 4.360 34.074 593 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.92 % Allowed : 16.67 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.36), residues: 534 helix: 1.25 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.57 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.001 0.000 HIS A 219 PHE 0.011 0.001 PHE C 181 TYR 0.007 0.001 TYR B 162 ARG 0.003 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 0.635 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.3780 (OUTLIER) cc_final: 0.2410 (m-80) REVERT: A 253 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8401 (tppt) REVERT: A 291 ASP cc_start: 0.7808 (p0) cc_final: 0.7526 (p0) REVERT: A 296 GLU cc_start: 0.4829 (tm-30) cc_final: 0.4256 (tt0) REVERT: B 162 TYR cc_start: 0.4320 (t80) cc_final: 0.1217 (m-10) REVERT: B 256 ARG cc_start: 0.7132 (tpp-160) cc_final: 0.6532 (ttm170) REVERT: C 162 TYR cc_start: 0.5194 (OUTLIER) cc_final: 0.4298 (p90) REVERT: C 216 ASP cc_start: 0.8381 (m-30) cc_final: 0.8068 (m-30) REVERT: C 256 ARG cc_start: 0.7532 (ttt90) cc_final: 0.6847 (ttm170) REVERT: C 257 THR cc_start: 0.9097 (m) cc_final: 0.8827 (p) REVERT: C 263 GLU cc_start: 0.7509 (tt0) cc_final: 0.7256 (tt0) REVERT: C 286 PRO cc_start: 0.8156 (Cg_exo) cc_final: 0.7955 (Cg_endo) REVERT: C 306 ASN cc_start: 0.7061 (m-40) cc_final: 0.6522 (p0) outliers start: 9 outliers final: 7 residues processed: 137 average time/residue: 0.3918 time to fit residues: 64.6883 Evaluate side-chains 138 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 233 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4431 Z= 0.186 Angle : 0.495 3.858 5988 Z= 0.260 Chirality : 0.034 0.141 663 Planarity : 0.005 0.041 777 Dihedral : 4.243 33.183 593 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.35 % Allowed : 15.60 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.36), residues: 534 helix: 1.30 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.60 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.001 0.000 HIS C 219 PHE 0.010 0.001 PHE C 181 TYR 0.005 0.001 TYR B 162 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.3786 (OUTLIER) cc_final: 0.2380 (m-80) REVERT: A 253 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8412 (mmtt) REVERT: A 291 ASP cc_start: 0.7846 (p0) cc_final: 0.7524 (p0) REVERT: A 296 GLU cc_start: 0.4815 (tm-30) cc_final: 0.4060 (tt0) REVERT: B 162 TYR cc_start: 0.4299 (t80) cc_final: 0.1240 (m-10) REVERT: B 256 ARG cc_start: 0.7179 (tpp-160) cc_final: 0.6532 (ttm170) REVERT: B 328 MET cc_start: 0.6217 (tpt) cc_final: 0.5798 (tpt) REVERT: C 162 TYR cc_start: 0.5182 (OUTLIER) cc_final: 0.4297 (p90) REVERT: C 216 ASP cc_start: 0.8342 (m-30) cc_final: 0.8061 (m-30) REVERT: C 256 ARG cc_start: 0.7557 (ttt90) cc_final: 0.6906 (ttm170) REVERT: C 257 THR cc_start: 0.9095 (m) cc_final: 0.8823 (p) REVERT: C 263 GLU cc_start: 0.7450 (tt0) cc_final: 0.7215 (tt0) REVERT: C 286 PRO cc_start: 0.8155 (Cg_exo) cc_final: 0.7954 (Cg_endo) outliers start: 11 outliers final: 8 residues processed: 141 average time/residue: 0.4001 time to fit residues: 68.4522 Evaluate side-chains 143 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 233 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4431 Z= 0.196 Angle : 0.516 4.658 5988 Z= 0.271 Chirality : 0.034 0.138 663 Planarity : 0.005 0.041 777 Dihedral : 4.181 32.552 593 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.14 % Allowed : 16.45 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.37), residues: 534 helix: 1.39 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.52 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.001 0.000 HIS C 219 PHE 0.010 0.001 PHE C 181 TYR 0.005 0.001 TYR B 162 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.3690 (OUTLIER) cc_final: 0.2255 (m-80) REVERT: A 263 GLU cc_start: 0.7122 (tt0) cc_final: 0.6907 (tt0) REVERT: A 291 ASP cc_start: 0.7824 (p0) cc_final: 0.7500 (p0) REVERT: A 296 GLU cc_start: 0.4806 (tm-30) cc_final: 0.4114 (tt0) REVERT: B 162 TYR cc_start: 0.4310 (t80) cc_final: 0.1258 (m-10) REVERT: B 256 ARG cc_start: 0.7191 (tpp-160) cc_final: 0.6532 (ttm170) REVERT: C 162 TYR cc_start: 0.5169 (OUTLIER) cc_final: 0.4281 (p90) REVERT: C 216 ASP cc_start: 0.8345 (m-30) cc_final: 0.8065 (m-30) REVERT: C 256 ARG cc_start: 0.7563 (ttt90) cc_final: 0.6910 (ttm170) REVERT: C 257 THR cc_start: 0.9098 (m) cc_final: 0.8822 (p) outliers start: 10 outliers final: 8 residues processed: 139 average time/residue: 0.3796 time to fit residues: 64.3214 Evaluate side-chains 141 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 233 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4431 Z= 0.191 Angle : 0.501 3.867 5988 Z= 0.263 Chirality : 0.034 0.141 663 Planarity : 0.005 0.042 777 Dihedral : 4.150 32.077 593 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.14 % Allowed : 16.24 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.37), residues: 534 helix: 1.44 (0.28), residues: 375 sheet: None (None), residues: 0 loop : 0.57 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.001 0.000 HIS A 219 PHE 0.010 0.001 PHE C 181 TYR 0.005 0.001 TYR B 162 ARG 0.005 0.000 ARG C 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.3508 (OUTLIER) cc_final: 0.2025 (m-80) REVERT: A 291 ASP cc_start: 0.7803 (p0) cc_final: 0.7488 (p0) REVERT: A 296 GLU cc_start: 0.4798 (tm-30) cc_final: 0.4101 (tt0) REVERT: B 162 TYR cc_start: 0.4350 (t80) cc_final: 0.1340 (m-10) REVERT: B 256 ARG cc_start: 0.7143 (tpp-160) cc_final: 0.6533 (ttm170) REVERT: B 283 ARG cc_start: 0.8600 (tpp-160) cc_final: 0.8241 (tpp80) REVERT: C 162 TYR cc_start: 0.5141 (OUTLIER) cc_final: 0.4250 (p90) REVERT: C 216 ASP cc_start: 0.8343 (m-30) cc_final: 0.8064 (m-30) REVERT: C 256 ARG cc_start: 0.7578 (ttt90) cc_final: 0.6918 (ttm170) REVERT: C 257 THR cc_start: 0.9127 (m) cc_final: 0.8855 (p) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.4212 time to fit residues: 69.1965 Evaluate side-chains 136 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 233 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 0.0270 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 0.4980 chunk 28 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.154827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129106 restraints weight = 24649.480| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 4.11 r_work: 0.3541 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4431 Z= 0.147 Angle : 0.479 3.747 5988 Z= 0.245 Chirality : 0.033 0.133 663 Planarity : 0.005 0.040 777 Dihedral : 3.895 29.533 593 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.64 % Allowed : 18.16 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.37), residues: 534 helix: 1.68 (0.28), residues: 375 sheet: None (None), residues: 0 loop : 0.78 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.000 0.000 HIS A 219 PHE 0.003 0.000 PHE B 168 TYR 0.005 0.001 TYR A 254 ARG 0.004 0.000 ARG C 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2684.51 seconds wall clock time: 46 minutes 56.63 seconds (2816.63 seconds total)