Starting phenix.real_space_refine on Fri Aug 22 23:47:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rb5_19026/08_2025/8rb5_19026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rb5_19026/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rb5_19026/08_2025/8rb5_19026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rb5_19026/08_2025/8rb5_19026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rb5_19026/08_2025/8rb5_19026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rb5_19026/08_2025/8rb5_19026.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.06, per 1000 atoms: 0.23 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: 0.78 Conformation dependent library (CDL) restraints added in 342.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.20 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: 1.79 Time building geometry restraints manager: 1.13 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: 0.01 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: 0.860 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: 0.050 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.690 ------------------------------------------------------------------------------- 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= 0.718 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 248 TYR 0.152 0.019 TYR A 162 PHE 0.051 0.015 PHE B 237 TRP 0.076 0.018 TRP B 309 HIS 0.007 0.005 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.01188 ( 4431) covalent geometry : angle 1.71928 ( 5988) hydrogen bonds : bond 0.18370 ( 244) hydrogen bonds : angle 8.08582 ( 732) *********************** 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 : 0.305 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: 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: 0.7851 (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: 0.8120 (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: 0.6709 (ttm170) outliers start: 3 outliers final: 0 residues processed: 211 average time/residue: 0.2511 time to fit residues: 61.3421 Evaluate side-chains 145 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.151117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124958 restraints weight = 24856.212| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 4.02 r_work: 0.3488 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4303 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= 0.184 Angle : 0.619 4.025 5988 Z= 0.336 Chirality : 0.036 0.158 663 Planarity : 0.006 0.039 777 Dihedral : 5.812 39.146 593 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.35 % Allowed : 11.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.34), residues: 534 helix: 0.09 (0.25), residues: 375 sheet: None (None), residues: 0 loop : 0.32 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 283 TYR 0.010 0.002 TYR B 162 PHE 0.013 0.002 PHE B 181 TRP 0.013 0.001 TRP C 184 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 4431) covalent geometry : angle 0.61851 ( 5988) hydrogen bonds : bond 0.04982 ( 244) hydrogen bonds : angle 5.55015 ( 732) *********************** 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: 11 poor density : 160 time to evaluate : 0.259 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: A 162 TYR cc_start: 0.4164 (OUTLIER) cc_final: 0.1907 (m-80) REVERT: A 218 MET cc_start: 0.9234 (tpp) cc_final: 0.8752 (tpt) REVERT: A 253 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8684 (mtmt) REVERT: A 291 ASP cc_start: 0.8288 (p0) cc_final: 0.7953 (p0) REVERT: A 296 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7721 (tm-30) REVERT: A 299 MET cc_start: 0.9131 (mtp) cc_final: 0.8708 (mpp) REVERT: B 162 TYR cc_start: 0.4904 (t80) cc_final: 0.0126 (m-10) REVERT: B 256 ARG cc_start: 0.7435 (tpp-160) cc_final: 0.6452 (ttm170) REVERT: C 216 ASP cc_start: 0.8693 (m-30) cc_final: 0.8481 (m-30) REVERT: C 256 ARG cc_start: 0.7673 (ttt90) cc_final: 0.6974 (ttm170) outliers start: 11 outliers final: 7 residues processed: 164 average time/residue: 0.1987 time to fit residues: 38.5464 Evaluate side-chains 153 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.151377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125460 restraints weight = 24667.728| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.98 r_work: 0.3512 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4431 Z= 0.128 Angle : 0.538 4.132 5988 Z= 0.285 Chirality : 0.035 0.138 663 Planarity : 0.005 0.044 777 Dihedral : 5.146 36.582 593 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.14 % Allowed : 13.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.35), residues: 534 helix: 0.68 (0.26), residues: 375 sheet: None (None), residues: 0 loop : 0.54 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 247 TYR 0.009 0.001 TYR B 162 PHE 0.010 0.001 PHE C 181 TRP 0.011 0.001 TRP C 184 HIS 0.001 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4431) covalent geometry : angle 0.53757 ( 5988) hydrogen bonds : bond 0.04045 ( 244) hydrogen bonds : angle 5.16889 ( 732) *********************** 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 165 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.234 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: 0.4080 (OUTLIER) cc_final: 0.1902 (m-80) REVERT: A 218 MET cc_start: 0.9197 (tpp) cc_final: 0.8606 (tpt) REVERT: A 253 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8664 (mtmt) REVERT: A 296 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7817 (tm-30) REVERT: B 162 TYR cc_start: 0.4359 (t80) cc_final: -0.0029 (m-80) REVERT: B 256 ARG cc_start: 0.7501 (tpp-160) cc_final: 0.6646 (ttm170) REVERT: C 256 ARG cc_start: 0.7767 (ttt90) cc_final: 0.7201 (ttm170) REVERT: C 328 MET cc_start: 0.7258 (tpp) cc_final: 0.6910 (tpt) outliers start: 10 outliers final: 5 residues processed: 159 average time/residue: 0.2476 time to fit residues: 45.9997 Evaluate side-chains 141 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 282 LYS 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 28 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.154535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129074 restraints weight = 24511.183| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.89 r_work: 0.3593 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4431 Z= 0.107 Angle : 0.500 3.760 5988 Z= 0.263 Chirality : 0.034 0.149 663 Planarity : 0.005 0.043 777 Dihedral : 4.722 34.412 593 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.07 % Allowed : 13.68 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.36), residues: 534 helix: 1.04 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.62 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 283 TYR 0.007 0.001 TYR C 162 PHE 0.007 0.001 PHE A 181 TRP 0.010 0.001 TRP C 184 HIS 0.001 0.000 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4431) covalent geometry : angle 0.49990 ( 5988) hydrogen bonds : bond 0.03600 ( 244) hydrogen bonds : angle 4.83843 ( 732) *********************** 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 151 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.200 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: 0.3922 (OUTLIER) cc_final: 0.1840 (m-80) REVERT: A 218 MET cc_start: 0.9182 (tpp) cc_final: 0.8596 (tpt) REVERT: A 253 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8655 (mtmt) REVERT: A 296 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7817 (tm-30) REVERT: B 162 TYR cc_start: 0.4275 (t80) cc_final: 0.0001 (m-80) REVERT: B 253 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8826 (mtmt) REVERT: B 256 ARG cc_start: 0.7474 (tpp-160) cc_final: 0.6525 (ttm170) REVERT: B 272 LEU cc_start: 0.8333 (tp) cc_final: 0.8077 (mt) REVERT: B 283 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8397 (tpp80) REVERT: C 256 ARG cc_start: 0.7766 (ttt90) cc_final: 0.7208 (ttm170) outliers start: 5 outliers final: 3 residues processed: 147 average time/residue: 0.1958 time to fit residues: 34.6852 Evaluate side-chains 135 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain C residue 191 ILE 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 35 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 0.1980 chunk 39 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.155492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129349 restraints weight = 24849.178| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 4.12 r_work: 0.3589 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5935 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= 0.113 Angle : 0.488 3.857 5988 Z= 0.256 Chirality : 0.034 0.142 663 Planarity : 0.005 0.045 777 Dihedral : 4.436 33.099 593 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.28 % Allowed : 15.17 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.36), residues: 534 helix: 1.22 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.63 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 283 TYR 0.006 0.001 TYR A 254 PHE 0.009 0.001 PHE A 181 TRP 0.009 0.001 TRP C 184 HIS 0.000 0.000 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 4431) covalent geometry : angle 0.48828 ( 5988) hydrogen bonds : bond 0.03413 ( 244) hydrogen bonds : angle 4.75831 ( 732) *********************** 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 145 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.240 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: 0.3813 (OUTLIER) cc_final: 0.1713 (m-80) REVERT: A 218 MET cc_start: 0.9188 (tpp) cc_final: 0.8599 (tpt) REVERT: A 296 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7800 (tm-30) REVERT: B 162 TYR cc_start: 0.4534 (t80) cc_final: 0.0443 (m-10) REVERT: B 256 ARG cc_start: 0.7454 (tpp-160) cc_final: 0.6743 (ttm170) REVERT: B 272 LEU cc_start: 0.8351 (tp) cc_final: 0.8132 (mt) REVERT: B 283 ARG cc_start: 0.8731 (ttm-80) cc_final: 0.8430 (tpp80) REVERT: C 256 ARG cc_start: 0.7819 (ttt90) cc_final: 0.7245 (ttm170) REVERT: C 272 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7868 (mt) REVERT: C 286 PRO cc_start: 0.8113 (Cg_exo) cc_final: 0.7877 (Cg_endo) outliers start: 6 outliers final: 2 residues processed: 141 average time/residue: 0.2073 time to fit residues: 34.9110 Evaluate side-chains 140 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.151878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126412 restraints weight = 24533.508| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.94 r_work: 0.3570 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4431 Z= 0.148 Angle : 0.508 4.015 5988 Z= 0.269 Chirality : 0.035 0.141 663 Planarity : 0.005 0.043 777 Dihedral : 4.365 33.473 593 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.92 % Allowed : 14.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.36), residues: 534 helix: 1.27 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.54 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 287 TYR 0.008 0.002 TYR B 162 PHE 0.012 0.001 PHE C 181 TRP 0.009 0.001 TRP C 184 HIS 0.001 0.000 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4431) covalent geometry : angle 0.50827 ( 5988) hydrogen bonds : bond 0.03513 ( 244) hydrogen bonds : angle 4.77349 ( 732) *********************** 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 143 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.263 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: 0.3879 (OUTLIER) cc_final: 0.1732 (m-80) REVERT: A 218 MET cc_start: 0.9211 (tpp) cc_final: 0.8940 (tpp) REVERT: A 296 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7796 (tm-30) REVERT: A 328 MET cc_start: 0.7497 (mmm) cc_final: 0.6659 (tpp) REVERT: B 162 TYR cc_start: 0.4565 (t80) cc_final: 0.0428 (m-10) REVERT: B 256 ARG cc_start: 0.7514 (tpp-160) cc_final: 0.6769 (ttm170) REVERT: C 162 TYR cc_start: 0.5360 (OUTLIER) cc_final: 0.4615 (p90) REVERT: C 256 ARG cc_start: 0.7840 (ttt90) cc_final: 0.7270 (ttm170) REVERT: C 286 PRO cc_start: 0.8163 (Cg_exo) cc_final: 0.7939 (Cg_endo) REVERT: C 306 ASN cc_start: 0.6853 (m-40) cc_final: 0.6507 (p0) outliers start: 9 outliers final: 3 residues processed: 136 average time/residue: 0.2090 time to fit residues: 34.1423 Evaluate side-chains 131 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR 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 28 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.150037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124629 restraints weight = 25080.370| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.98 r_work: 0.3480 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 4431 Z= 0.279 Angle : 0.611 4.508 5988 Z= 0.331 Chirality : 0.038 0.147 663 Planarity : 0.006 0.046 777 Dihedral : 4.697 35.238 593 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.50 % Allowed : 15.81 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.35), residues: 534 helix: 0.86 (0.26), residues: 369 sheet: None (None), residues: 0 loop : 0.33 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.016 0.003 TYR B 162 PHE 0.018 0.002 PHE B 181 TRP 0.007 0.001 TRP C 184 HIS 0.003 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 4431) covalent geometry : angle 0.61071 ( 5988) hydrogen bonds : bond 0.04328 ( 244) hydrogen bonds : angle 5.24876 ( 732) *********************** 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 131 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.249 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: 0.3826 (OUTLIER) cc_final: 0.1525 (m-80) REVERT: A 296 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7684 (tm-30) REVERT: B 162 TYR cc_start: 0.4845 (t80) cc_final: 0.0575 (m-10) REVERT: B 256 ARG cc_start: 0.7657 (tpp-160) cc_final: 0.6670 (ttm170) REVERT: C 162 TYR cc_start: 0.5398 (OUTLIER) cc_final: 0.4586 (p90) REVERT: C 256 ARG cc_start: 0.7920 (ttt90) cc_final: 0.7266 (ttm170) REVERT: C 286 PRO cc_start: 0.8342 (Cg_exo) cc_final: 0.8139 (Cg_endo) outliers start: 7 outliers final: 5 residues processed: 126 average time/residue: 0.2222 time to fit residues: 33.4039 Evaluate side-chains 124 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR 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 233 CYS Chi-restraints excluded: chain C residue 272 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.152807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127563 restraints weight = 24712.519| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.98 r_work: 0.3526 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.6321 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= 0.139 Angle : 0.507 4.043 5988 Z= 0.267 Chirality : 0.035 0.139 663 Planarity : 0.005 0.045 777 Dihedral : 4.441 34.132 593 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.92 % Allowed : 16.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.36), residues: 534 helix: 1.05 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.43 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 211 TYR 0.007 0.001 TYR B 162 PHE 0.009 0.001 PHE C 181 TRP 0.010 0.001 TRP C 184 HIS 0.001 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4431) covalent geometry : angle 0.50716 ( 5988) hydrogen bonds : bond 0.03546 ( 244) hydrogen bonds : angle 4.80699 ( 732) *********************** 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 139 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.220 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: 0.3787 (OUTLIER) cc_final: 0.1505 (m-80) REVERT: A 296 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7670 (tm-30) REVERT: B 162 TYR cc_start: 0.4625 (t80) cc_final: 0.0538 (m-10) REVERT: B 177 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8730 (pm20) REVERT: B 256 ARG cc_start: 0.7568 (tpp-160) cc_final: 0.6629 (ttm170) REVERT: C 162 TYR cc_start: 0.5356 (OUTLIER) cc_final: 0.4649 (p90) REVERT: C 211 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7735 (ttm-80) REVERT: C 256 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7267 (ttm170) REVERT: C 286 PRO cc_start: 0.8288 (Cg_exo) cc_final: 0.8076 (Cg_endo) outliers start: 9 outliers final: 4 residues processed: 133 average time/residue: 0.2074 time to fit residues: 33.0911 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 : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 243 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.149989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124664 restraints weight = 24745.575| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.93 r_work: 0.3499 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4431 Z= 0.220 Angle : 0.571 4.532 5988 Z= 0.306 Chirality : 0.036 0.142 663 Planarity : 0.006 0.050 777 Dihedral : 4.534 32.904 593 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.50 % Allowed : 17.74 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.36), residues: 534 helix: 0.88 (0.26), residues: 375 sheet: None (None), residues: 0 loop : 0.35 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 247 TYR 0.012 0.002 TYR B 162 PHE 0.015 0.002 PHE C 181 TRP 0.008 0.001 TRP C 184 HIS 0.001 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 4431) covalent geometry : angle 0.57051 ( 5988) hydrogen bonds : bond 0.03938 ( 244) hydrogen bonds : angle 5.09166 ( 732) *********************** 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 126 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.176 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: 0.3657 (OUTLIER) cc_final: 0.1250 (m-80) REVERT: A 194 GLU cc_start: 0.8612 (tt0) cc_final: 0.8133 (tm-30) REVERT: A 296 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7674 (tm-30) REVERT: A 328 MET cc_start: 0.7629 (mmm) cc_final: 0.6855 (tpp) REVERT: B 162 TYR cc_start: 0.4738 (t80) cc_final: 0.0513 (m-10) REVERT: B 177 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8776 (pm20) REVERT: B 256 ARG cc_start: 0.7627 (tpp-160) cc_final: 0.6663 (ttm170) REVERT: B 283 ARG cc_start: 0.8934 (tpp-160) cc_final: 0.8625 (tpp80) REVERT: C 162 TYR cc_start: 0.5421 (OUTLIER) cc_final: 0.4644 (p90) REVERT: C 201 GLU cc_start: 0.8291 (mp0) cc_final: 0.8053 (tp30) REVERT: C 211 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7696 (ttm-80) REVERT: C 256 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7259 (ttm170) REVERT: C 286 PRO cc_start: 0.8372 (Cg_exo) cc_final: 0.8165 (Cg_endo) outliers start: 7 outliers final: 5 residues processed: 122 average time/residue: 0.1752 time to fit residues: 25.9102 Evaluate side-chains 125 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 243 SER 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 Chi-restraints excluded: chain C residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.0270 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.154522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129538 restraints weight = 24560.736| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.99 r_work: 0.3554 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.6477 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= 0.104 Angle : 0.504 3.837 5988 Z= 0.264 Chirality : 0.034 0.146 663 Planarity : 0.005 0.043 777 Dihedral : 4.287 31.958 593 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.85 % Allowed : 18.80 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.36), residues: 534 helix: 1.14 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.61 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 247 TYR 0.007 0.001 TYR C 258 PHE 0.006 0.001 PHE C 237 TRP 0.012 0.001 TRP C 184 HIS 0.001 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4431) covalent geometry : angle 0.50422 ( 5988) hydrogen bonds : bond 0.03267 ( 244) hydrogen bonds : angle 4.64452 ( 732) ********************** 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 132 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.192 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: 0.3710 (OUTLIER) cc_final: 0.1397 (m-80) REVERT: A 177 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8504 (mp0) REVERT: A 194 GLU cc_start: 0.8592 (tt0) cc_final: 0.8054 (tm-30) REVERT: A 218 MET cc_start: 0.9262 (tpp) cc_final: 0.9000 (tpt) REVERT: A 296 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7815 (tm-30) REVERT: B 162 TYR cc_start: 0.4575 (t80) cc_final: 0.0459 (m-80) REVERT: B 256 ARG cc_start: 0.7552 (tpp-160) cc_final: 0.6616 (ttm170) REVERT: C 162 TYR cc_start: 0.5345 (OUTLIER) cc_final: 0.4675 (p90) REVERT: C 201 GLU cc_start: 0.8278 (mp0) cc_final: 0.8076 (tp30) REVERT: C 256 ARG cc_start: 0.7871 (ttt90) cc_final: 0.7242 (ttm170) REVERT: C 286 PRO cc_start: 0.8306 (Cg_exo) cc_final: 0.8091 (Cg_endo) outliers start: 4 outliers final: 2 residues processed: 129 average time/residue: 0.1461 time to fit residues: 22.9732 Evaluate side-chains 127 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 190 GLU 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 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.154741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129555 restraints weight = 24517.388| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 4.00 r_work: 0.3553 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.6578 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= 0.120 Angle : 0.521 4.467 5988 Z= 0.272 Chirality : 0.035 0.159 663 Planarity : 0.005 0.045 777 Dihedral : 4.192 29.941 593 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.85 % Allowed : 18.59 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.37), residues: 534 helix: 1.24 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.65 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 247 TYR 0.004 0.001 TYR B 258 PHE 0.009 0.001 PHE A 181 TRP 0.010 0.001 TRP C 184 HIS 0.001 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4431) covalent geometry : angle 0.52089 ( 5988) hydrogen bonds : bond 0.03269 ( 244) hydrogen bonds : angle 4.66337 ( 732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2285.76 seconds wall clock time: 39 minutes 22.50 seconds (2362.50 seconds total)