Starting phenix.real_space_refine on Thu Mar 13 04:59:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rb5_19026/03_2025/8rb5_19026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rb5_19026/03_2025/8rb5_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/cci-nas-00/data/ceres_data/8rb5_19026/03_2025/8rb5_19026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rb5_19026/03_2025/8rb5_19026.map" model { file = "/net/cci-nas-00/data/ceres_data/8rb5_19026/03_2025/8rb5_19026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rb5_19026/03_2025/8rb5_19026.cif" } 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. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.96, per 1000 atoms: 0.57 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 715.8 milliseconds 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: 0.77 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: 2.65 Time building geometry restraints manager: 2.88 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: 0.00 - 2.58: 13753 2.58 - 5.16: 1790 5.16 - 7.75: 506 7.75 - 10.33: 25 10.33 - 12.91: 9 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 2.450 nonbonded pdb=" HG SER B 266 " pdb=" OE1 GLU B 335 " model vdw 1.632 2.450 nonbonded pdb=" HG SER B 229 " pdb=" OE1 GLU B 232 " model vdw 1.633 2.450 nonbonded pdb=" O VAL C 206 " pdb=" HG SER C 209 " model vdw 1.665 2.450 nonbonded pdb=" O VAL B 206 " pdb=" HG SER B 209 " model vdw 1.666 2.450 ... (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 Time spend for trying shortcut: 0.02 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: 0.440 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: 0.160 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 22.810 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 0.745 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: 0.5188 time to fit residues: 127.1105 Evaluate side-chains 144 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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: 5.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.150740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124895 restraints weight = 24702.433| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 4.03 r_work: 0.3490 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4431 Z= 0.245 Angle : 0.627 4.154 5988 Z= 0.339 Chirality : 0.036 0.143 663 Planarity : 0.006 0.037 777 Dihedral : 5.736 39.046 593 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.56 % Allowed : 11.11 % 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: 0.05 (0.34), residues: 534 helix: 0.07 (0.25), residues: 375 sheet: None (None), residues: 0 loop : 0.35 (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 B 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 171 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.664 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: A 162 TYR cc_start: 0.4170 (OUTLIER) cc_final: 0.1909 (m-80) REVERT: A 218 MET cc_start: 0.9237 (tpp) cc_final: 0.8758 (tpt) REVERT: A 253 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8685 (mtmt) REVERT: A 291 ASP cc_start: 0.8328 (p0) cc_final: 0.7989 (p0) REVERT: A 296 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7731 (tm-30) REVERT: B 256 ARG cc_start: 0.7452 (tpp-160) cc_final: 0.6468 (ttm170) REVERT: C 216 ASP cc_start: 0.8698 (m-30) cc_final: 0.8493 (m-30) REVERT: C 256 ARG cc_start: 0.7690 (ttt90) cc_final: 0.7008 (ttm170) outliers start: 12 outliers final: 9 residues processed: 164 average time/residue: 0.4619 time to fit residues: 89.4733 Evaluate side-chains 152 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 304 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 233 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.148197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122190 restraints weight = 25032.070| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.99 r_work: 0.3502 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4431 Z= 0.187 Angle : 0.540 4.149 5988 Z= 0.287 Chirality : 0.035 0.135 663 Planarity : 0.005 0.043 777 Dihedral : 5.144 36.971 593 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.56 % Allowed : 12.61 % Favored : 84.83 % 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: 0.76 (0.35), residues: 534 helix: 0.66 (0.26), residues: 375 sheet: None (None), residues: 0 loop : 0.44 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 184 HIS 0.001 0.001 HIS C 219 PHE 0.010 0.001 PHE A 181 TYR 0.007 0.001 TYR B 162 ARG 0.005 0.000 ARG B 311 *********************** 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 169 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.721 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: 0.4184 (OUTLIER) cc_final: 0.1988 (m-80) REVERT: A 218 MET cc_start: 0.9200 (tpp) cc_final: 0.8650 (tpt) REVERT: A 253 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8663 (mtmt) REVERT: A 296 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7821 (tm-30) REVERT: B 162 TYR cc_start: 0.4647 (t80) cc_final: 0.3465 (t80) REVERT: B 256 ARG cc_start: 0.7494 (tpp-160) cc_final: 0.6622 (ttm170) REVERT: C 256 ARG cc_start: 0.7777 (ttt90) cc_final: 0.7219 (ttm170) REVERT: C 328 MET cc_start: 0.7235 (tpp) cc_final: 0.6908 (tpt) outliers start: 12 outliers final: 8 residues processed: 161 average time/residue: 0.4834 time to fit residues: 91.2367 Evaluate side-chains 143 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 233 CYS Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 282 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.152890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127881 restraints weight = 24524.583| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.83 r_work: 0.3548 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5680 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= 0.263 Angle : 0.546 4.161 5988 Z= 0.293 Chirality : 0.035 0.145 663 Planarity : 0.005 0.044 777 Dihedral : 4.911 36.583 593 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.35 % Allowed : 14.32 % 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: 0.94 (0.35), residues: 534 helix: 0.86 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.34 (0.46), 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 0.014 0.002 PHE B 181 TYR 0.009 0.002 TYR B 162 ARG 0.003 0.000 ARG B 283 *********************** 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 147 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.727 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: 0.3981 (OUTLIER) cc_final: 0.1872 (m-80) REVERT: A 218 MET cc_start: 0.9221 (tpp) cc_final: 0.8862 (tpp) REVERT: A 253 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8693 (mtmt) REVERT: A 296 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7695 (tm-30) REVERT: B 253 LYS cc_start: 0.9169 (ttmt) cc_final: 0.8852 (mtmt) REVERT: B 256 ARG cc_start: 0.7547 (tpp-160) cc_final: 0.6725 (ttm170) REVERT: B 283 ARG cc_start: 0.8748 (ttm-80) cc_final: 0.8419 (tpp80) REVERT: C 256 ARG cc_start: 0.7821 (ttt90) cc_final: 0.7247 (ttm170) REVERT: C 286 PRO cc_start: 0.8251 (Cg_exo) cc_final: 0.7969 (Cg_endo) outliers start: 11 outliers final: 5 residues processed: 142 average time/residue: 0.4330 time to fit residues: 73.3559 Evaluate side-chains 133 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 282 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.154052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.128891 restraints weight = 24470.566| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.91 r_work: 0.3562 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4431 Z= 0.190 Angle : 0.507 3.763 5988 Z= 0.267 Chirality : 0.035 0.140 663 Planarity : 0.005 0.044 777 Dihedral : 4.611 35.695 593 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.71 % Allowed : 14.32 % Favored : 83.97 % 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: 1.12 (0.35), residues: 534 helix: 0.98 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.45 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.001 0.000 HIS B 219 PHE 0.009 0.001 PHE C 181 TYR 0.007 0.001 TYR B 162 ARG 0.004 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 142 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.757 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: 0.4012 (OUTLIER) cc_final: 0.1868 (m-80) REVERT: A 296 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7824 (tm-30) REVERT: B 162 TYR cc_start: 0.4623 (t80) cc_final: 0.0548 (m-10) REVERT: B 256 ARG cc_start: 0.7501 (tpp-160) cc_final: 0.6710 (ttm170) REVERT: B 272 LEU cc_start: 0.8332 (tp) cc_final: 0.7892 (tp) REVERT: B 283 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8463 (tpp80) REVERT: C 162 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.4582 (p90) REVERT: C 211 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7557 (ttm-80) REVERT: C 256 ARG cc_start: 0.7894 (ttt90) cc_final: 0.7278 (ttm170) REVERT: C 286 PRO cc_start: 0.8231 (Cg_exo) cc_final: 0.7907 (Cg_endo) REVERT: C 306 ASN cc_start: 0.6898 (m-40) cc_final: 0.6562 (p0) outliers start: 8 outliers final: 4 residues processed: 137 average time/residue: 0.4300 time to fit residues: 70.8486 Evaluate side-chains 132 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 186 GLU 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 282 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.128014 restraints weight = 24593.974| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.92 r_work: 0.3537 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4431 Z= 0.279 Angle : 0.549 4.404 5988 Z= 0.294 Chirality : 0.036 0.146 663 Planarity : 0.005 0.044 777 Dihedral : 4.580 35.066 593 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.92 % Allowed : 15.17 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.36), residues: 534 helix: 0.99 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.34 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.001 0.001 HIS C 219 PHE 0.013 0.002 PHE C 181 TYR 0.011 0.002 TYR B 162 ARG 0.003 0.000 ARG C 211 *********************** 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 137 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.728 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: A 162 TYR cc_start: 0.4120 (OUTLIER) cc_final: 0.1897 (m-80) REVERT: A 296 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7831 (tm-30) REVERT: B 162 TYR cc_start: 0.4727 (t80) cc_final: 0.0571 (m-10) REVERT: B 256 ARG cc_start: 0.7538 (tpp-160) cc_final: 0.6795 (ttm170) REVERT: B 283 ARG cc_start: 0.8803 (ttm-80) cc_final: 0.8543 (tpp-160) REVERT: C 162 TYR cc_start: 0.5357 (OUTLIER) cc_final: 0.4561 (p90) REVERT: C 256 ARG cc_start: 0.7931 (ttt90) cc_final: 0.7316 (ttm170) REVERT: C 286 PRO cc_start: 0.8199 (Cg_exo) cc_final: 0.7991 (Cg_endo) REVERT: C 306 ASN cc_start: 0.6986 (m-40) cc_final: 0.6508 (p0) REVERT: C 328 MET cc_start: 0.7167 (tpp) cc_final: 0.6906 (tpt) outliers start: 9 outliers final: 6 residues processed: 132 average time/residue: 0.4232 time to fit residues: 67.1390 Evaluate side-chains 133 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 295 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 282 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.152641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127420 restraints weight = 24684.536| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.96 r_work: 0.3518 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4431 Z= 0.232 Angle : 0.518 4.050 5988 Z= 0.275 Chirality : 0.035 0.147 663 Planarity : 0.005 0.044 777 Dihedral : 4.475 34.506 593 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.71 % Allowed : 16.24 % 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: 1.13 (0.36), residues: 534 helix: 1.02 (0.27), residues: 369 sheet: None (None), residues: 0 loop : 0.39 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.001 0.000 HIS B 219 PHE 0.011 0.001 PHE C 181 TYR 0.009 0.001 TYR B 162 ARG 0.002 0.000 ARG C 211 *********************** 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 134 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.683 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: A 162 TYR cc_start: 0.3996 (OUTLIER) cc_final: 0.1787 (m-80) REVERT: A 218 MET cc_start: 0.9336 (tpp) cc_final: 0.9101 (tpt) REVERT: A 296 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7824 (tm-30) REVERT: B 162 TYR cc_start: 0.4663 (t80) cc_final: 0.0520 (m-10) REVERT: B 256 ARG cc_start: 0.7582 (tpp-160) cc_final: 0.6825 (ttm170) REVERT: B 272 LEU cc_start: 0.8302 (tp) cc_final: 0.7900 (tp) REVERT: B 283 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8584 (tpp-160) REVERT: B 328 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6486 (tpt) REVERT: C 162 TYR cc_start: 0.5394 (OUTLIER) cc_final: 0.4602 (p90) REVERT: C 256 ARG cc_start: 0.7914 (ttt90) cc_final: 0.7248 (ttm170) REVERT: C 263 GLU cc_start: 0.7543 (tt0) cc_final: 0.7241 (tt0) REVERT: C 286 PRO cc_start: 0.8223 (Cg_exo) cc_final: 0.8019 (Cg_endo) REVERT: C 306 ASN cc_start: 0.6992 (m-40) cc_final: 0.6530 (p0) REVERT: C 328 MET cc_start: 0.7141 (tpp) cc_final: 0.6886 (tpt) outliers start: 8 outliers final: 3 residues processed: 129 average time/residue: 0.4339 time to fit residues: 67.8563 Evaluate side-chains 129 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain C residue 162 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.154220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128359 restraints weight = 25577.497| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 4.21 r_work: 0.3522 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6355 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= 0.201 Angle : 0.501 3.971 5988 Z= 0.265 Chirality : 0.035 0.142 663 Planarity : 0.005 0.046 777 Dihedral : 4.343 33.147 593 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.71 % Allowed : 16.45 % Favored : 81.84 % 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: 1.28 (0.36), residues: 534 helix: 1.12 (0.27), residues: 369 sheet: None (None), residues: 0 loop : 0.47 (0.48), residues: 165 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 0.010 0.001 PHE C 181 TYR 0.007 0.001 TYR B 162 ARG 0.002 0.000 ARG C 211 *********************** 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 140 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.723 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: 0.3909 (OUTLIER) cc_final: 0.1724 (m-80) REVERT: A 296 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7829 (tm-30) REVERT: B 162 TYR cc_start: 0.4700 (t80) cc_final: 0.0429 (m-80) REVERT: B 177 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8759 (pm20) REVERT: B 253 LYS cc_start: 0.9051 (ttpt) cc_final: 0.8804 (mtmt) REVERT: B 256 ARG cc_start: 0.7588 (tpp-160) cc_final: 0.6815 (ttm170) REVERT: B 272 LEU cc_start: 0.8320 (tp) cc_final: 0.7895 (tp) REVERT: B 283 ARG cc_start: 0.8826 (ttm-80) cc_final: 0.8612 (tpp-160) REVERT: C 162 TYR cc_start: 0.5404 (OUTLIER) cc_final: 0.4620 (p90) REVERT: C 256 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7275 (ttm170) REVERT: C 263 GLU cc_start: 0.7503 (tt0) cc_final: 0.7203 (tt0) REVERT: C 286 PRO cc_start: 0.8229 (Cg_exo) cc_final: 0.8018 (Cg_endo) REVERT: C 306 ASN cc_start: 0.7059 (m-40) cc_final: 0.6598 (p0) REVERT: C 328 MET cc_start: 0.7260 (tpp) cc_final: 0.7014 (tpt) outliers start: 8 outliers final: 4 residues processed: 134 average time/residue: 0.4383 time to fit residues: 71.0822 Evaluate side-chains 128 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 295 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 162 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.155718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130623 restraints weight = 24872.950| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 4.04 r_work: 0.3562 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4431 Z= 0.150 Angle : 0.491 4.245 5988 Z= 0.256 Chirality : 0.034 0.141 663 Planarity : 0.005 0.044 777 Dihedral : 4.204 31.324 593 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.64 % Allowed : 17.74 % 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: 1.50 (0.36), residues: 534 helix: 1.24 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.67 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.000 0.000 HIS C 219 PHE 0.005 0.001 PHE C 181 TYR 0.006 0.001 TYR C 258 ARG 0.007 0.000 ARG B 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 134 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.694 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: A 162 TYR cc_start: 0.3832 (OUTLIER) cc_final: 0.1780 (m-80) REVERT: A 177 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8474 (mp0) REVERT: A 194 GLU cc_start: 0.8544 (tt0) cc_final: 0.7975 (tm-30) REVERT: A 218 MET cc_start: 0.9293 (tpp) cc_final: 0.9044 (tpt) REVERT: A 296 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7695 (tm-30) REVERT: B 162 TYR cc_start: 0.4520 (t80) cc_final: 0.0489 (m-80) REVERT: B 177 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8771 (pm20) REVERT: B 253 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8755 (mtmt) REVERT: B 256 ARG cc_start: 0.7499 (tpp-160) cc_final: 0.6789 (ttm170) REVERT: B 272 LEU cc_start: 0.8284 (tp) cc_final: 0.7845 (tp) REVERT: B 283 ARG cc_start: 0.8786 (ttm-80) cc_final: 0.8508 (tpp80) REVERT: C 162 TYR cc_start: 0.5323 (OUTLIER) cc_final: 0.4568 (p90) REVERT: C 256 ARG cc_start: 0.7907 (ttt90) cc_final: 0.7288 (ttm170) REVERT: C 286 PRO cc_start: 0.8276 (Cg_exo) cc_final: 0.8038 (Cg_endo) outliers start: 3 outliers final: 1 residues processed: 132 average time/residue: 0.4206 time to fit residues: 67.6509 Evaluate side-chains 129 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 162 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.0470 chunk 18 optimal weight: 4.9990 overall best weight: 1.9282 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.152555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127191 restraints weight = 24535.269| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.97 r_work: 0.3553 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.6500 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= 0.175 Angle : 0.498 3.809 5988 Z= 0.262 Chirality : 0.034 0.137 663 Planarity : 0.005 0.043 777 Dihedral : 4.106 30.121 593 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.43 % Allowed : 18.38 % 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: 1.62 (0.37), residues: 534 helix: 1.32 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.73 (0.51), 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 0.009 0.001 PHE C 181 TYR 0.006 0.001 TYR C 268 ARG 0.006 0.000 ARG B 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 131 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.741 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: A 162 TYR cc_start: 0.3773 (m-80) cc_final: 0.1592 (m-80) REVERT: A 177 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8499 (mp0) REVERT: A 194 GLU cc_start: 0.8531 (tt0) cc_final: 0.7926 (tm-30) REVERT: A 218 MET cc_start: 0.9285 (tpp) cc_final: 0.9070 (tpt) REVERT: A 296 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7814 (tm-30) REVERT: B 162 TYR cc_start: 0.4500 (t80) cc_final: 0.0473 (m-80) REVERT: B 256 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.6835 (ttm170) REVERT: B 258 TYR cc_start: 0.8314 (m-80) cc_final: 0.8045 (m-80) REVERT: B 272 LEU cc_start: 0.8293 (tp) cc_final: 0.7863 (tp) REVERT: B 283 ARG cc_start: 0.8769 (ttm-80) cc_final: 0.8493 (tpp80) REVERT: C 162 TYR cc_start: 0.5231 (OUTLIER) cc_final: 0.4456 (p90) REVERT: C 256 ARG cc_start: 0.7900 (ttt90) cc_final: 0.7116 (ttm170) REVERT: C 286 PRO cc_start: 0.8300 (Cg_exo) cc_final: 0.8076 (Cg_endo) outliers start: 2 outliers final: 1 residues processed: 130 average time/residue: 0.4377 time to fit residues: 69.5046 Evaluate side-chains 124 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 162 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.155869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.130522 restraints weight = 24675.262| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 4.06 r_work: 0.3572 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4431 Z= 0.156 Angle : 0.497 4.522 5988 Z= 0.258 Chirality : 0.034 0.139 663 Planarity : 0.005 0.043 777 Dihedral : 3.828 14.714 591 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.43 % Allowed : 18.16 % 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: 1.67 (0.37), residues: 534 helix: 1.37 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.74 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.000 0.000 HIS B 219 PHE 0.006 0.001 PHE C 181 TYR 0.011 0.001 TYR A 254 ARG 0.006 0.000 ARG B 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4746.48 seconds wall clock time: 82 minutes 27.86 seconds (4947.86 seconds total)