Starting phenix.real_space_refine on Fri Sep 11 00:34:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq4_32085/09_2026/7vq4_32085.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq4_32085/09_2026/7vq4_32085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vq4_32085/09_2026/7vq4_32085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq4_32085/09_2026/7vq4_32085.map" model { file = "/net/cci-nas-00/data/ceres_data/7vq4_32085/09_2026/7vq4_32085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq4_32085/09_2026/7vq4_32085.cif" } resolution = 3.2 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= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4070 2.51 5 N 1052 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6306 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Time building chain proxies: 1.65, per 1000 atoms: 0.26 Number of scatterers: 6306 At special positions: 0 Unit cell: (82.134, 84.162, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1150 8.00 N 1052 7.00 C 4070 6.00 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: 0.49 Conformation dependent library (CDL) restraints added in 394.5 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.624A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.863A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 69 through 102 removed outlier: 3.756A pdb=" N THR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 134 removed outlier: 3.524A pdb=" N LYS A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.601A pdb=" N SER A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 183 Processing helix chain 'A' and resid 187 through 214 removed outlier: 3.694A pdb=" N ASP A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.615A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 267 through 293 removed outlier: 3.720A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.833A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.738A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 removed outlier: 4.368A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 398 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.624A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.864A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 69 through 102 removed outlier: 3.757A pdb=" N THR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.523A pdb=" N LYS B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.601A pdb=" N SER B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 183 Processing helix chain 'B' and resid 187 through 214 removed outlier: 3.693A pdb=" N ASP B 191 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.615A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 Processing helix chain 'B' and resid 267 through 293 removed outlier: 3.720A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.833A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.737A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 removed outlier: 4.368A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 398 509 hydrogen bonds defined for protein. 1527 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: 0.69 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2008 1.34 - 1.46: 1045 1.46 - 1.57: 3321 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6434 Sorted by residual: bond pdb=" CB TRP B 57 " pdb=" CG TRP B 57 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CB TRP A 57 " pdb=" CG TRP A 57 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB TRP B 187 " pdb=" CG TRP B 187 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.63e+00 bond pdb=" CB TRP A 187 " pdb=" CG TRP A 187 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.62e+00 bond pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 1.527 1.518 0.009 8.50e-03 1.38e+04 1.14e+00 ... (remaining 6429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 8313 1.50 - 3.01: 299 3.01 - 4.51: 56 4.51 - 6.01: 20 6.01 - 7.52: 4 Bond angle restraints: 8692 Sorted by residual: angle pdb=" N VAL B 105 " pdb=" CA VAL B 105 " pdb=" C VAL B 105 " ideal model delta sigma weight residual 112.17 108.66 3.51 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N VAL A 105 " pdb=" CA VAL A 105 " pdb=" C VAL A 105 " ideal model delta sigma weight residual 112.17 108.67 3.50 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N PHE B 134 " pdb=" CA PHE B 134 " pdb=" C PHE B 134 " ideal model delta sigma weight residual 110.44 114.21 -3.77 1.20e+00 6.94e-01 9.89e+00 angle pdb=" N PHE A 134 " pdb=" CA PHE A 134 " pdb=" C PHE A 134 " ideal model delta sigma weight residual 110.44 114.16 -3.72 1.20e+00 6.94e-01 9.62e+00 angle pdb=" CA PRO B 267 " pdb=" C PRO B 267 " pdb=" O PRO B 267 " ideal model delta sigma weight residual 123.07 119.36 3.71 1.38e+00 5.25e-01 7.22e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 3396 18.03 - 36.05: 366 36.05 - 54.08: 62 54.08 - 72.10: 26 72.10 - 90.13: 6 Dihedral angle restraints: 3856 sinusoidal: 1532 harmonic: 2324 Sorted by residual: dihedral pdb=" CA CYS A 184 " pdb=" C CYS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA CYS B 184 " pdb=" C CYS B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta harmonic sigma weight residual -180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA HIS B 259 " pdb=" C HIS B 259 " pdb=" N GLY B 260 " pdb=" CA GLY B 260 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 499 0.030 - 0.060: 357 0.060 - 0.090: 105 0.090 - 0.119: 30 0.119 - 0.149: 5 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA PRO B 365 " pdb=" N PRO B 365 " pdb=" C PRO B 365 " pdb=" CB PRO B 365 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA PRO A 365 " pdb=" N PRO A 365 " pdb=" C PRO A 365 " pdb=" CB PRO A 365 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 332 " pdb=" N ILE A 332 " pdb=" C ILE A 332 " pdb=" CB ILE A 332 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 993 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 365 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 364 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 365 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 127 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 128 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 128 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 128 " 0.021 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 239 2.70 - 3.25: 6944 3.25 - 3.80: 10031 3.80 - 4.35: 11847 4.35 - 4.90: 20167 Nonbonded interactions: 49228 Sorted by model distance: nonbonded pdb=" OD1 ASP A 295 " pdb=" N PHE A 296 " model vdw 2.155 3.120 nonbonded pdb=" OD1 ASP B 295 " pdb=" N PHE B 296 " model vdw 2.155 3.120 nonbonded pdb=" O MET B 1 " pdb=" N ARG B 5 " model vdw 2.178 3.120 nonbonded pdb=" OH TYR A 291 " pdb=" OG SER B 376 " model vdw 2.209 3.040 nonbonded pdb=" NH1 ARG A 80 " pdb=" OH TYR A 136 " model vdw 2.225 3.120 ... (remaining 49223 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' } 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: 0.540 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.007 0.044 6434 Z= 0.317 Angle : 0.740 7.518 8692 Z= 0.423 Chirality : 0.042 0.149 996 Planarity : 0.004 0.050 1090 Dihedral : 16.105 90.127 2352 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.30 % Allowed : 8.62 % Favored : 89.08 % 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 are not related in a simple way. whole: -1.96 (0.27), residues: 792 helix: -0.72 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -3.76 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 13 TYR 0.013 0.002 TYR B 291 PHE 0.018 0.002 PHE B 153 TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.32 ( 6434) covalent geometry : angle 0.73974 / 0.42 ( 8692) hydrogen bonds : bond 0.12719 / 8.28 ( 509) hydrogen bonds : angle 5.74557 / 4.22 ( 1527) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.247 Fit side-chains REVERT: A 40 TYR cc_start: 0.8043 (t80) cc_final: 0.7503 (t80) REVERT: A 180 SER cc_start: 0.9004 (t) cc_final: 0.8580 (p) REVERT: A 237 LYS cc_start: 0.8450 (mttt) cc_final: 0.8150 (mtmt) REVERT: A 306 LEU cc_start: 0.8688 (tp) cc_final: 0.8481 (tp) REVERT: A 307 GLU cc_start: 0.7515 (pt0) cc_final: 0.7258 (pm20) REVERT: A 322 LYS cc_start: 0.7820 (tptm) cc_final: 0.7412 (ttpt) REVERT: B 1 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4477 (ptp) REVERT: B 40 TYR cc_start: 0.8064 (t80) cc_final: 0.7540 (t80) REVERT: B 328 LEU cc_start: 0.9183 (tp) cc_final: 0.8902 (tp) outliers start: 16 outliers final: 7 residues processed: 216 average time/residue: 0.0995 time to fit residues: 26.9752 Evaluate side-chains 162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 223 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 HIS A 54 ASN A 251 ASN A 259 HIS A 293 ASN A 340 HIS A 343 ASN B 24 HIS B 54 ASN B 259 HIS B 280 GLN B 293 ASN B 330 GLN B 340 HIS B 343 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.158761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130194 restraints weight = 9378.621| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.63 r_work: 0.3605 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6434 Z= 0.142 Angle : 0.556 5.780 8692 Z= 0.293 Chirality : 0.038 0.146 996 Planarity : 0.004 0.046 1090 Dihedral : 5.485 50.362 870 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.74 % Allowed : 15.66 % Favored : 79.60 % 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 are not related in a simple way. whole: 1.25 (0.30), residues: 792 helix: 1.59 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -3.18 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 265 TYR 0.013 0.001 TYR B 236 PHE 0.013 0.001 PHE A 145 TRP 0.009 0.001 TRP A 57 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 6434) covalent geometry : angle 0.55602 / 0.29 ( 8692) hydrogen bonds : bond 0.05174 / 3.40 ( 509) hydrogen bonds : angle 3.92526 / 2.90 ( 1527) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8405 (pp30) REVERT: A 105 VAL cc_start: 0.6425 (OUTLIER) cc_final: 0.6055 (t) REVERT: A 159 MET cc_start: 0.7039 (ptt) cc_final: 0.6610 (mtm) REVERT: A 180 SER cc_start: 0.8999 (t) cc_final: 0.8438 (p) REVERT: A 193 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7056 (t-90) REVERT: A 201 ASP cc_start: 0.8322 (t0) cc_final: 0.8052 (t0) REVERT: A 237 LYS cc_start: 0.8369 (mttt) cc_final: 0.7996 (mtmt) REVERT: A 263 ARG cc_start: 0.8039 (tpp80) cc_final: 0.7180 (tmt170) REVERT: A 286 ASP cc_start: 0.8632 (t70) cc_final: 0.8362 (t0) REVERT: A 321 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7597 (mmt) REVERT: A 322 LYS cc_start: 0.7649 (tptm) cc_final: 0.6999 (ttpt) REVERT: A 368 MET cc_start: 0.8116 (mmm) cc_final: 0.7906 (mmm) REVERT: B 1 MET cc_start: 0.4605 (ttt) cc_final: 0.4179 (tpp) REVERT: B 9 ARG cc_start: 0.6167 (mtt-85) cc_final: 0.5416 (ptp90) REVERT: B 154 ARG cc_start: 0.7495 (mtp-110) cc_final: 0.7245 (mtm110) REVERT: B 193 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7206 (t-90) REVERT: B 201 ASP cc_start: 0.8298 (t0) cc_final: 0.8010 (t0) REVERT: B 328 LEU cc_start: 0.9038 (tp) cc_final: 0.8614 (tp) REVERT: B 377 MET cc_start: 0.8621 (mmt) cc_final: 0.8276 (mmm) outliers start: 33 outliers final: 20 residues processed: 190 average time/residue: 0.0795 time to fit residues: 19.9056 Evaluate side-chains 177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.0618 > 50:) chunk 27 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 12 optimal weight: 0.0570 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN B 208 GLN B 251 ASN B 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.156317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127851 restraints weight = 9864.298| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.48 r_work: 0.3616 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6434 Z= 0.163 Angle : 0.569 5.966 8692 Z= 0.296 Chirality : 0.037 0.159 996 Planarity : 0.004 0.050 1090 Dihedral : 4.643 36.709 866 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.03 % Allowed : 16.81 % Favored : 77.16 % 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 are not related in a simple way. whole: 1.91 (0.30), residues: 792 helix: 2.00 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.92 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 265 TYR 0.011 0.001 TYR B 236 PHE 0.013 0.001 PHE B 141 TRP 0.008 0.001 TRP B 129 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 6434) covalent geometry : angle 0.56936 / 0.30 ( 8692) hydrogen bonds : bond 0.05448 / 3.57 ( 509) hydrogen bonds : angle 3.83066 / 2.82 ( 1527) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8435 (pp30) REVERT: A 105 VAL cc_start: 0.6572 (OUTLIER) cc_final: 0.6255 (t) REVERT: A 159 MET cc_start: 0.7092 (ptt) cc_final: 0.6636 (mtm) REVERT: A 193 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7266 (t-90) REVERT: A 201 ASP cc_start: 0.8310 (t0) cc_final: 0.8040 (t0) REVERT: A 322 LYS cc_start: 0.7603 (tptm) cc_final: 0.6926 (ttpt) REVERT: A 377 MET cc_start: 0.8552 (mmt) cc_final: 0.8286 (mmm) REVERT: B 1 MET cc_start: 0.5212 (ttt) cc_final: 0.4644 (tpp) REVERT: B 90 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7599 (mp) REVERT: B 154 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.7354 (mtm110) REVERT: B 193 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.7334 (t-90) REVERT: B 286 ASP cc_start: 0.8581 (t70) cc_final: 0.8369 (t0) REVERT: B 328 LEU cc_start: 0.9054 (tp) cc_final: 0.8666 (tp) REVERT: B 377 MET cc_start: 0.8576 (mmt) cc_final: 0.8194 (mmm) outliers start: 42 outliers final: 30 residues processed: 184 average time/residue: 0.0707 time to fit residues: 17.7479 Evaluate side-chains 180 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 69 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 GLN A 266 HIS A 289 ASN A 297 GLN B 266 HIS B 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.155418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126829 restraints weight = 9896.015| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.52 r_work: 0.3607 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6434 Z= 0.169 Angle : 0.577 6.201 8692 Z= 0.298 Chirality : 0.038 0.178 996 Planarity : 0.004 0.049 1090 Dihedral : 4.526 28.597 866 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 6.47 % Allowed : 18.82 % Favored : 74.71 % 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 are not related in a simple way. whole: 2.22 (0.30), residues: 792 helix: 2.16 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -2.55 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 265 TYR 0.014 0.001 TYR A 236 PHE 0.013 0.001 PHE B 141 TRP 0.009 0.001 TRP B 129 HIS 0.003 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 6434) covalent geometry : angle 0.57689 / 0.30 ( 8692) hydrogen bonds : bond 0.05403 / 3.55 ( 509) hydrogen bonds : angle 3.79937 / 2.80 ( 1527) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8440 (pp30) REVERT: A 159 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6656 (mtm) REVERT: A 193 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7300 (t-90) REVERT: A 201 ASP cc_start: 0.8317 (t0) cc_final: 0.8032 (t0) REVERT: A 322 LYS cc_start: 0.7559 (tptm) cc_final: 0.6867 (ttpt) REVERT: A 377 MET cc_start: 0.8552 (mmt) cc_final: 0.8269 (mmm) REVERT: B 1 MET cc_start: 0.5735 (ttt) cc_final: 0.5113 (tpp) REVERT: B 154 ARG cc_start: 0.7615 (mtp-110) cc_final: 0.7361 (mtm110) REVERT: B 193 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7357 (t-90) REVERT: B 286 ASP cc_start: 0.8600 (t70) cc_final: 0.8389 (t0) REVERT: B 328 LEU cc_start: 0.9006 (tp) cc_final: 0.8662 (tp) outliers start: 45 outliers final: 27 residues processed: 174 average time/residue: 0.0719 time to fit residues: 17.0016 Evaluate side-chains 172 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.0070 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.159418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131163 restraints weight = 9851.407| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.51 r_work: 0.3659 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6434 Z= 0.128 Angle : 0.559 10.684 8692 Z= 0.284 Chirality : 0.037 0.230 996 Planarity : 0.004 0.048 1090 Dihedral : 4.128 22.737 865 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.17 % Allowed : 19.97 % Favored : 74.86 % 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 are not related in a simple way. whole: 2.70 (0.30), residues: 792 helix: 2.48 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -2.30 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 265 TYR 0.014 0.001 TYR A 236 PHE 0.011 0.001 PHE B 141 TRP 0.009 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 6434) covalent geometry : angle 0.55926 / 0.28 ( 8692) hydrogen bonds : bond 0.04555 / 3.00 ( 509) hydrogen bonds : angle 3.58956 / 2.66 ( 1527) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7189 (t-90) REVERT: A 96 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8431 (pp30) REVERT: A 159 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6695 (mtm) REVERT: A 193 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7088 (t-90) REVERT: A 201 ASP cc_start: 0.8297 (t0) cc_final: 0.8093 (t0) REVERT: A 322 LYS cc_start: 0.7525 (tptm) cc_final: 0.6783 (ttpt) REVERT: A 377 MET cc_start: 0.8373 (mmt) cc_final: 0.8133 (mmm) REVERT: A 405 MET cc_start: 0.3027 (mpp) cc_final: 0.2404 (mmp) REVERT: B 1 MET cc_start: 0.5553 (ttt) cc_final: 0.4932 (tpp) REVERT: B 106 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: B 154 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.7266 (mtm110) REVERT: B 193 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7094 (t-90) REVERT: B 328 LEU cc_start: 0.8888 (tp) cc_final: 0.8494 (tp) outliers start: 36 outliers final: 24 residues processed: 170 average time/residue: 0.0671 time to fit residues: 16.0364 Evaluate side-chains 166 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 79 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.158670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130976 restraints weight = 9483.432| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.54 r_work: 0.3626 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6434 Z= 0.122 Angle : 0.556 7.951 8692 Z= 0.280 Chirality : 0.037 0.204 996 Planarity : 0.003 0.050 1090 Dihedral : 3.945 23.149 862 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.89 % Allowed : 19.68 % Favored : 74.43 % 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 are not related in a simple way. whole: 2.92 (0.31), residues: 792 helix: 2.60 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.12 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 265 TYR 0.014 0.001 TYR A 236 PHE 0.012 0.001 PHE B 145 TRP 0.009 0.001 TRP B 129 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 6434) covalent geometry : angle 0.55553 / 0.28 ( 8692) hydrogen bonds : bond 0.04258 / 2.81 ( 509) hydrogen bonds : angle 3.48917 / 2.59 ( 1527) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8109 (OUTLIER) cc_final: 0.7075 (t-90) REVERT: A 96 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8400 (pp30) REVERT: A 159 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6659 (mtm) REVERT: A 193 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.6855 (t-90) REVERT: A 201 ASP cc_start: 0.8356 (t0) cc_final: 0.8068 (t0) REVERT: A 237 LYS cc_start: 0.8353 (mttt) cc_final: 0.8071 (mmmt) REVERT: A 322 LYS cc_start: 0.7393 (tptm) cc_final: 0.6598 (ttpt) REVERT: A 328 LEU cc_start: 0.8328 (tp) cc_final: 0.8033 (tp) REVERT: A 405 MET cc_start: 0.2844 (mpp) cc_final: 0.2272 (mmp) REVERT: B 1 MET cc_start: 0.5693 (ttt) cc_final: 0.5158 (tpp) REVERT: B 154 ARG cc_start: 0.7518 (mtp-110) cc_final: 0.7170 (mtm110) REVERT: B 193 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.6950 (t-90) outliers start: 41 outliers final: 29 residues processed: 176 average time/residue: 0.0677 time to fit residues: 16.5300 Evaluate side-chains 173 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 0.0570 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN B 345 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.158906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131429 restraints weight = 9576.727| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.57 r_work: 0.3630 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6434 Z= 0.125 Angle : 0.594 12.980 8692 Z= 0.292 Chirality : 0.037 0.198 996 Planarity : 0.003 0.050 1090 Dihedral : 3.938 23.640 862 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.46 % Allowed : 21.84 % Favored : 72.70 % 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 are not related in a simple way. whole: 3.01 (0.31), residues: 792 helix: 2.65 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.99 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 265 TYR 0.013 0.001 TYR A 236 PHE 0.011 0.001 PHE A 206 TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 6434) covalent geometry : angle 0.59434 / 0.29 ( 8692) hydrogen bonds : bond 0.04197 / 2.77 ( 509) hydrogen bonds : angle 3.45471 / 2.56 ( 1527) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7050 (t-90) REVERT: A 96 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8394 (pp30) REVERT: A 159 MET cc_start: 0.7099 (ptt) cc_final: 0.6610 (mtm) REVERT: A 193 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.6927 (t-90) REVERT: A 201 ASP cc_start: 0.8326 (t0) cc_final: 0.7998 (t0) REVERT: A 237 LYS cc_start: 0.8341 (mttt) cc_final: 0.8113 (mmmt) REVERT: A 321 MET cc_start: 0.7796 (mmp) cc_final: 0.7571 (mmt) REVERT: A 322 LYS cc_start: 0.7516 (tptm) cc_final: 0.6635 (ttpt) REVERT: A 328 LEU cc_start: 0.8235 (tp) cc_final: 0.7899 (tp) REVERT: A 405 MET cc_start: 0.2934 (mpp) cc_final: 0.2486 (mmp) REVERT: B 1 MET cc_start: 0.5669 (ttt) cc_final: 0.5410 (tpp) REVERT: B 106 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6313 (tt0) REVERT: B 154 ARG cc_start: 0.7484 (mtp-110) cc_final: 0.7143 (mtm110) REVERT: B 193 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.7044 (t-90) REVERT: B 284 ARG cc_start: 0.7899 (mpt90) cc_final: 0.7606 (mpt90) REVERT: B 331 MET cc_start: 0.8358 (mmm) cc_final: 0.8045 (mmm) outliers start: 38 outliers final: 28 residues processed: 174 average time/residue: 0.0737 time to fit residues: 17.6137 Evaluate side-chains 179 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.158170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131426 restraints weight = 9609.101| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.52 r_work: 0.3644 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6434 Z= 0.126 Angle : 0.608 14.441 8692 Z= 0.296 Chirality : 0.037 0.204 996 Planarity : 0.004 0.049 1090 Dihedral : 3.932 23.562 862 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.03 % Allowed : 22.84 % Favored : 72.13 % 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 are not related in a simple way. whole: 3.02 (0.31), residues: 792 helix: 2.64 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.88 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 9 TYR 0.013 0.001 TYR A 236 PHE 0.015 0.001 PHE B 145 TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 6434) covalent geometry : angle 0.60803 / 0.30 ( 8692) hydrogen bonds : bond 0.04214 / 2.78 ( 509) hydrogen bonds : angle 3.44864 / 2.56 ( 1527) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7067 (t-90) REVERT: A 96 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8387 (pp30) REVERT: A 159 MET cc_start: 0.6956 (ptt) cc_final: 0.6491 (mtm) REVERT: A 193 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.6921 (t-90) REVERT: A 201 ASP cc_start: 0.8332 (t0) cc_final: 0.8001 (t0) REVERT: A 237 LYS cc_start: 0.8353 (mttt) cc_final: 0.8137 (mmmt) REVERT: A 322 LYS cc_start: 0.7510 (tptm) cc_final: 0.6653 (ttpt) REVERT: A 328 LEU cc_start: 0.8259 (tp) cc_final: 0.7962 (tp) REVERT: A 405 MET cc_start: 0.2767 (mpp) cc_final: 0.2324 (mmp) REVERT: B 1 MET cc_start: 0.6011 (ttt) cc_final: 0.5409 (tpp) REVERT: B 154 ARG cc_start: 0.7475 (mtp-110) cc_final: 0.7147 (mtm110) REVERT: B 193 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7065 (t-90) REVERT: B 307 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7304 (pm20) REVERT: B 323 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7995 (mt-10) REVERT: B 377 MET cc_start: 0.8566 (mmt) cc_final: 0.8248 (mmm) outliers start: 35 outliers final: 25 residues processed: 170 average time/residue: 0.0764 time to fit residues: 17.6965 Evaluate side-chains 166 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 307 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.152919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125239 restraints weight = 9490.872| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.56 r_work: 0.3534 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6434 Z= 0.187 Angle : 0.692 14.207 8692 Z= 0.338 Chirality : 0.039 0.208 996 Planarity : 0.004 0.049 1090 Dihedral : 4.171 21.654 862 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.60 % Allowed : 23.71 % Favored : 71.70 % 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 are not related in a simple way. whole: 2.67 (0.30), residues: 792 helix: 2.38 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.84 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 9 TYR 0.012 0.002 TYR A 236 PHE 0.013 0.002 PHE A 206 TRP 0.008 0.001 TRP B 187 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 6434) covalent geometry : angle 0.69171 / 0.34 ( 8692) hydrogen bonds : bond 0.05493 / 3.59 ( 509) hydrogen bonds : angle 3.74179 / 2.77 ( 1527) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7410 (t-90) REVERT: A 96 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8425 (pp30) REVERT: A 159 MET cc_start: 0.7060 (ptt) cc_final: 0.6610 (mtm) REVERT: A 193 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7336 (t-90) REVERT: A 201 ASP cc_start: 0.8392 (t0) cc_final: 0.8072 (t0) REVERT: A 322 LYS cc_start: 0.7550 (tptm) cc_final: 0.6766 (ttpt) REVERT: A 405 MET cc_start: 0.3008 (mpp) cc_final: 0.2530 (mmp) REVERT: B 17 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7905 (mt-10) REVERT: B 154 ARG cc_start: 0.7615 (mtp-110) cc_final: 0.7282 (mtm110) REVERT: B 193 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7536 (t-90) REVERT: B 286 ASP cc_start: 0.8551 (t0) cc_final: 0.8342 (t70) REVERT: B 307 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: B 377 MET cc_start: 0.8680 (mmt) cc_final: 0.8380 (mmm) outliers start: 32 outliers final: 24 residues processed: 168 average time/residue: 0.0732 time to fit residues: 17.0459 Evaluate side-chains 167 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.154213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126943 restraints weight = 9515.126| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.47 r_work: 0.3593 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6434 Z= 0.147 Angle : 0.646 14.647 8692 Z= 0.315 Chirality : 0.038 0.198 996 Planarity : 0.004 0.048 1090 Dihedral : 4.113 24.751 862 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.45 % Allowed : 23.99 % Favored : 71.55 % 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 are not related in a simple way. whole: 2.79 (0.31), residues: 792 helix: 2.47 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.82 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 9 TYR 0.014 0.001 TYR A 236 PHE 0.011 0.001 PHE B 141 TRP 0.009 0.001 TRP B 129 HIS 0.004 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6434) covalent geometry : angle 0.64618 / 0.32 ( 8692) hydrogen bonds : bond 0.04807 / 3.16 ( 509) hydrogen bonds : angle 3.63107 / 2.69 ( 1527) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7253 (t-90) REVERT: A 96 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8459 (pp30) REVERT: A 159 MET cc_start: 0.7036 (ptt) cc_final: 0.6582 (mtm) REVERT: A 193 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7159 (t-90) REVERT: A 201 ASP cc_start: 0.8353 (t0) cc_final: 0.8113 (t0) REVERT: A 322 LYS cc_start: 0.7540 (tptm) cc_final: 0.6726 (ttpt) REVERT: A 375 VAL cc_start: 0.9294 (t) cc_final: 0.9005 (m) REVERT: A 405 MET cc_start: 0.2835 (mpp) cc_final: 0.2373 (mmp) REVERT: B 154 ARG cc_start: 0.7503 (mtp-110) cc_final: 0.7199 (mtm110) REVERT: B 193 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7321 (t-90) REVERT: B 307 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: B 377 MET cc_start: 0.8620 (mmt) cc_final: 0.8326 (mmm) outliers start: 31 outliers final: 23 residues processed: 160 average time/residue: 0.0640 time to fit residues: 14.3864 Evaluate side-chains 161 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 307 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128334 restraints weight = 9506.331| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.47 r_work: 0.3598 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6434 Z= 0.146 Angle : 0.675 14.531 8692 Z= 0.323 Chirality : 0.038 0.201 996 Planarity : 0.004 0.047 1090 Dihedral : 4.117 24.978 862 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.31 % Allowed : 24.43 % Favored : 71.26 % 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 are not related in a simple way. whole: 2.85 (0.31), residues: 792 helix: 2.50 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.80 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 9 TYR 0.013 0.001 TYR A 236 PHE 0.010 0.001 PHE B 141 TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6434) covalent geometry : angle 0.67547 / 0.32 ( 8692) hydrogen bonds : bond 0.04758 / 3.12 ( 509) hydrogen bonds : angle 3.60276 / 2.68 ( 1527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1416.96 seconds wall clock time: 25 minutes 6.93 seconds (1506.93 seconds total)