Starting phenix.real_space_refine on Wed Aug 5 01:36:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9enf_19833/08_2026/9enf_19833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9enf_19833/08_2026/9enf_19833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9enf_19833/08_2026/9enf_19833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9enf_19833/08_2026/9enf_19833.map" model { file = "/net/cci-nas-00/data/ceres_data/9enf_19833/08_2026/9enf_19833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9enf_19833/08_2026/9enf_19833.cif" } resolution = 2.97 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= 0.003 sd= 0.015 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 P 180 5.49 5 S 28 5.16 5 C 4522 2.51 5 N 1450 2.21 5 O 2055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8235 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2083 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain breaks: 4 Chain: "B" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2270 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 4 Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1941 Classifications: {'RNA': 91} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 38} Link IDs: {'rna2p': 20, 'rna3p': 70} Chain: "D" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1941 Classifications: {'RNA': 91} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 38} Link IDs: {'rna2p': 20, 'rna3p': 70} Time building chain proxies: 1.89, per 1000 atoms: 0.23 Number of scatterers: 8235 At special positions: 0 Unit cell: (103.2, 147.92, 83.42, 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 28 16.00 P 180 15.00 O 2055 8.00 N 1450 7.00 C 4522 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: 0.44 Conformation dependent library (CDL) restraints added in 329.2 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1014 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 34.7% alpha, 19.2% beta 50 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 205 through 214 removed outlier: 3.691A pdb=" N MET A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.601A pdb=" N ASN A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 338 through 369 removed outlier: 3.714A pdb=" N GLU A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 100 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.860A pdb=" N ARG B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 213 through 217 removed outlier: 3.703A pdb=" N TYR B 216 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 217 " --> pdb=" O GLN B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 217' Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 277 through 291 Processing helix chain 'B' and resid 297 through 304 removed outlier: 3.696A pdb=" N GLU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 369 removed outlier: 3.661A pdb=" N PHE B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 removed outlier: 6.741A pdb=" N GLY A 61 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG A 133 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG A 63 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP A 131 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 65 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER A 129 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 67 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A 127 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE A 69 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 125 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 123 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASP A 326 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN A 126 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR A 194 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 269 " --> pdb=" O TYR A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA3, first strand: chain 'B' and resid 173 through 178 removed outlier: 5.623A pdb=" N ILE B 174 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B 70 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA B 176 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 68 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 178 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR B 71 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE B 124 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 326 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN B 126 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR B 194 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 239 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS B 220 " --> pdb=" O ARG B 239 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 128 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1699 1.33 - 1.45: 2964 1.45 - 1.57: 3724 1.57 - 1.69: 360 1.69 - 1.81: 44 Bond restraints: 8791 Sorted by residual: bond pdb=" C3' C D 23 " pdb=" O3' C D 23 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.20e-02 6.94e+03 1.99e+00 bond pdb=" C3' A D 61 " pdb=" O3' A D 61 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.20e-02 6.94e+03 1.98e+00 bond pdb=" C3' C C 23 " pdb=" O3' C C 23 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.20e-02 6.94e+03 1.97e+00 bond pdb=" N9 A D 56 " pdb=" C4 A D 56 " ideal model delta sigma weight residual 1.374 1.382 -0.008 6.00e-03 2.78e+04 1.89e+00 bond pdb=" C3' A C 61 " pdb=" O3' A C 61 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.20e-02 6.94e+03 1.85e+00 ... (remaining 8786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 12074 1.79 - 3.58: 644 3.58 - 5.37: 46 5.37 - 7.16: 10 7.16 - 8.95: 1 Bond angle restraints: 12775 Sorted by residual: angle pdb=" N1 C D 23 " pdb=" C2 C D 23 " pdb=" O2 C D 23 " ideal model delta sigma weight residual 118.90 122.06 -3.16 6.00e-01 2.78e+00 2.78e+01 angle pdb=" O5' A D 62 " pdb=" C5' A D 62 " pdb=" C4' A D 62 " ideal model delta sigma weight residual 109.40 113.61 -4.21 8.00e-01 1.56e+00 2.77e+01 angle pdb=" N1 C C 23 " pdb=" C2 C C 23 " pdb=" O2 C C 23 " ideal model delta sigma weight residual 118.90 122.00 -3.10 6.00e-01 2.78e+00 2.67e+01 angle pdb=" O5' A C 62 " pdb=" C5' A C 62 " pdb=" C4' A C 62 " ideal model delta sigma weight residual 109.40 113.52 -4.12 8.00e-01 1.56e+00 2.65e+01 angle pdb=" C1' C C 23 " pdb=" N1 C C 23 " pdb=" C2 C C 23 " ideal model delta sigma weight residual 118.80 124.10 -5.30 1.10e+00 8.26e-01 2.32e+01 ... (remaining 12770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 4921 35.45 - 70.90: 536 70.90 - 106.35: 67 106.35 - 141.81: 0 141.81 - 177.26: 8 Dihedral angle restraints: 5532 sinusoidal: 3974 harmonic: 1558 Sorted by residual: dihedral pdb=" O4' C C 23 " pdb=" C1' C C 23 " pdb=" N1 C C 23 " pdb=" C2 C C 23 " ideal model delta sinusoidal sigma weight residual 232.00 75.14 156.86 1 1.70e+01 3.46e-03 6.38e+01 dihedral pdb=" O4' C D 23 " pdb=" C1' C D 23 " pdb=" N1 C D 23 " pdb=" C2 C D 23 " ideal model delta sinusoidal sigma weight residual 232.00 75.40 156.60 1 1.70e+01 3.46e-03 6.37e+01 dihedral pdb=" O4' G C 48 " pdb=" C1' G C 48 " pdb=" N9 G C 48 " pdb=" C4 G C 48 " ideal model delta sinusoidal sigma weight residual -106.00 -171.32 65.32 1 1.70e+01 3.46e-03 1.94e+01 ... (remaining 5529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1112 0.043 - 0.087: 228 0.087 - 0.130: 120 0.130 - 0.173: 90 0.173 - 0.217: 7 Chirality restraints: 1557 Sorted by residual: chirality pdb=" C3' A C 61 " pdb=" C4' A C 61 " pdb=" O3' A C 61 " pdb=" C2' A C 61 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C3' A D 61 " pdb=" C4' A D 61 " pdb=" O3' A D 61 " pdb=" C2' A D 61 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C3' C D 23 " pdb=" C4' C D 23 " pdb=" O3' C D 23 " pdb=" C2' C D 23 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 1554 not shown) Planarity restraints: 955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 74 " -0.017 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP A 74 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 74 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 74 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 74 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 74 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 74 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 74 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 74 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A 74 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 260 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.88e+00 pdb=" N PRO A 261 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 320 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO B 321 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 321 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 321 " 0.023 5.00e-02 4.00e+02 ... (remaining 952 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 421 2.67 - 3.23: 7502 3.23 - 3.79: 14786 3.79 - 4.34: 18493 4.34 - 4.90: 26964 Nonbonded interactions: 68166 Sorted by model distance: nonbonded pdb=" O6 G C 30 " pdb=" O4 U C 57 " model vdw 2.114 2.432 nonbonded pdb=" OH TYR B 197 " pdb=" O VAL B 318 " model vdw 2.163 3.040 nonbonded pdb=" O SER A 185 " pdb=" OG SER A 189 " model vdw 2.172 3.040 nonbonded pdb=" O2' G C 64 " pdb=" OP1 U C 66 " model vdw 2.180 3.040 nonbonded pdb=" O2' G D 64 " pdb=" OP1 U D 66 " model vdw 2.182 3.040 ... (remaining 68161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 58 through 228 or resid 234 through 369)) selection = (chain 'B' and (resid 58 through 289 or resid 319 through 328 or resid 337 throu \ gh 369)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.390 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.670 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 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 : 0.003 0.036 8791 Z= 0.204 Angle : 0.767 8.953 12775 Z= 0.588 Chirality : 0.055 0.217 1557 Planarity : 0.004 0.042 955 Dihedral : 24.216 177.257 4518 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -1.68 (0.36), residues: 510 helix: 0.39 (0.43), residues: 154 sheet: -0.61 (0.53), residues: 93 loop : -2.31 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 280 TYR 0.020 0.002 TYR A 276 PHE 0.009 0.001 PHE B 184 TRP 0.059 0.004 TRP A 74 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.20 ( 8791) covalent geometry : angle 0.76683 / 0.59 (12775) hydrogen bonds : bond 0.13766 / 9.97 ( 290) hydrogen bonds : angle 5.23570 / 3.78 ( 661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: B 316 MET cc_start: 0.4995 (tpt) cc_final: 0.4640 (tpt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.4682 time to fit residues: 19.3066 Evaluate side-chains 27 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 50.0000 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.107838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.084741 restraints weight = 37270.109| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.91 r_work: 0.3878 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8791 Z= 0.204 Angle : 0.664 7.176 12775 Z= 0.354 Chirality : 0.043 0.382 1557 Planarity : 0.005 0.051 955 Dihedral : 25.135 171.732 3465 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.29 % Allowed : 11.37 % Favored : 87.34 % 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 are not related in a simple way. whole: -2.08 (0.34), residues: 510 helix: 0.56 (0.44), residues: 141 sheet: -0.69 (0.57), residues: 79 loop : -2.75 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 193 TYR 0.027 0.002 TYR A 276 PHE 0.013 0.002 PHE A 55 TRP 0.033 0.003 TRP A 74 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 ( 8791) covalent geometry : angle 0.66356 / 0.35 (12775) hydrogen bonds : bond 0.07976 / 5.13 ( 290) hydrogen bonds : angle 4.71253 / 3.33 ( 661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.214 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 31 average time/residue: 0.4804 time to fit residues: 16.2076 Evaluate side-chains 30 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 40.0000 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 50.0000 chunk 52 optimal weight: 50.0000 chunk 27 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.107758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.084924 restraints weight = 37174.528| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.00 r_work: 0.3880 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8791 Z= 0.167 Angle : 0.614 7.459 12775 Z= 0.330 Chirality : 0.042 0.388 1557 Planarity : 0.005 0.048 955 Dihedral : 25.142 171.449 3465 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.72 % Allowed : 13.95 % Favored : 84.33 % 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 are not related in a simple way. whole: -2.08 (0.34), residues: 510 helix: 0.64 (0.43), residues: 141 sheet: -0.90 (0.56), residues: 80 loop : -2.72 (0.31), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 173 TYR 0.028 0.002 TYR A 276 PHE 0.010 0.002 PHE B 267 TRP 0.029 0.003 TRP A 74 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 8791) covalent geometry : angle 0.61381 / 0.33 (12775) hydrogen bonds : bond 0.07399 / 4.76 ( 290) hydrogen bonds : angle 4.54134 / 3.21 ( 661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.4838 (mmp) cc_final: 0.4595 (mmt) outliers start: 8 outliers final: 2 residues processed: 32 average time/residue: 0.4201 time to fit residues: 14.6170 Evaluate side-chains 29 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 45 optimal weight: 0.0870 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.108885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.086158 restraints weight = 37632.715| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 3.02 r_work: 0.3917 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8791 Z= 0.119 Angle : 0.564 8.471 12775 Z= 0.303 Chirality : 0.040 0.384 1557 Planarity : 0.004 0.045 955 Dihedral : 25.040 171.496 3465 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.00 % Allowed : 14.38 % Favored : 82.62 % 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 are not related in a simple way. whole: -1.72 (0.36), residues: 510 helix: 0.94 (0.44), residues: 147 sheet: -0.69 (0.59), residues: 75 loop : -2.54 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.022 0.002 TYR A 276 PHE 0.010 0.001 PHE B 184 TRP 0.019 0.003 TRP A 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 8791) covalent geometry : angle 0.56395 / 0.30 (12775) hydrogen bonds : bond 0.06449 / 4.19 ( 290) hydrogen bonds : angle 4.21819 / 2.97 ( 661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.4776 (mmp) cc_final: 0.4573 (mmt) REVERT: B 361 MET cc_start: 0.6235 (ptp) cc_final: 0.5804 (tmm) outliers start: 14 outliers final: 3 residues processed: 39 average time/residue: 0.3757 time to fit residues: 16.0453 Evaluate side-chains 29 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 0.0970 chunk 39 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 overall best weight: 3.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.107043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.084128 restraints weight = 37858.448| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.05 r_work: 0.3862 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8791 Z= 0.187 Angle : 0.640 8.315 12775 Z= 0.338 Chirality : 0.042 0.395 1557 Planarity : 0.005 0.049 955 Dihedral : 25.075 171.324 3465 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.58 % Allowed : 17.17 % Favored : 80.26 % 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: -2.23 (0.34), residues: 510 helix: 0.45 (0.43), residues: 147 sheet: -1.05 (0.54), residues: 80 loop : -2.83 (0.30), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.029 0.002 TYR A 276 PHE 0.012 0.002 PHE A 55 TRP 0.017 0.003 TRP A 352 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 ( 8791) covalent geometry : angle 0.63965 / 0.34 (12775) hydrogen bonds : bond 0.07560 / 4.81 ( 290) hydrogen bonds : angle 4.47982 / 3.13 ( 661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.207 Fit side-chains REVERT: A 209 MET cc_start: 0.5097 (mmp) cc_final: 0.4874 (mmt) outliers start: 12 outliers final: 6 residues processed: 38 average time/residue: 0.3863 time to fit residues: 16.1753 Evaluate side-chains 33 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 13 optimal weight: 0.0010 chunk 52 optimal weight: 50.0000 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 60 optimal weight: 40.0000 chunk 66 optimal weight: 50.0000 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.105637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.082692 restraints weight = 37319.783| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.92 r_work: 0.3836 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8791 Z= 0.242 Angle : 0.698 8.117 12775 Z= 0.369 Chirality : 0.044 0.387 1557 Planarity : 0.006 0.053 955 Dihedral : 25.181 170.168 3465 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 2.79 % Allowed : 19.53 % Favored : 77.68 % 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: -2.54 (0.33), residues: 510 helix: 0.21 (0.43), residues: 142 sheet: -1.37 (0.54), residues: 80 loop : -2.93 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 173 TYR 0.040 0.003 TYR A 276 PHE 0.016 0.002 PHE A 55 TRP 0.061 0.005 TRP A 74 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.24 ( 8791) covalent geometry : angle 0.69813 / 0.37 (12775) hydrogen bonds : bond 0.08544 / 5.45 ( 290) hydrogen bonds : angle 4.82192 / 3.38 ( 661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.218 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 37 average time/residue: 0.4157 time to fit residues: 16.9150 Evaluate side-chains 36 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 50.0000 chunk 27 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 50.0000 chunk 41 optimal weight: 4.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.105479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.082410 restraints weight = 37639.000| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.98 r_work: 0.3832 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8791 Z= 0.227 Angle : 0.709 13.321 12775 Z= 0.372 Chirality : 0.045 0.381 1557 Planarity : 0.006 0.053 955 Dihedral : 25.212 169.814 3465 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.43 % Allowed : 20.60 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.66 (0.33), residues: 510 helix: 0.10 (0.42), residues: 142 sheet: -1.32 (0.55), residues: 77 loop : -3.03 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 173 TYR 0.043 0.003 TYR A 276 PHE 0.016 0.002 PHE B 124 TRP 0.088 0.006 TRP A 74 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 ( 8791) covalent geometry : angle 0.70945 / 0.37 (12775) hydrogen bonds : bond 0.08483 / 5.44 ( 290) hydrogen bonds : angle 4.84058 / 3.38 ( 661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.225 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 42 average time/residue: 0.4185 time to fit residues: 19.2755 Evaluate side-chains 38 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 65 optimal weight: 50.0000 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 50.0000 chunk 64 optimal weight: 50.0000 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.106706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.083710 restraints weight = 37727.991| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.99 r_work: 0.3870 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8791 Z= 0.163 Angle : 0.669 13.360 12775 Z= 0.348 Chirality : 0.042 0.380 1557 Planarity : 0.005 0.052 955 Dihedral : 25.163 169.913 3465 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.22 % Allowed : 21.46 % Favored : 75.32 % 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 are not related in a simple way. whole: -2.44 (0.34), residues: 510 helix: 0.16 (0.42), residues: 148 sheet: -1.26 (0.58), residues: 71 loop : -2.83 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 173 TYR 0.035 0.002 TYR A 276 PHE 0.025 0.002 PHE A 124 TRP 0.080 0.006 TRP A 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 8791) covalent geometry : angle 0.66866 / 0.35 (12775) hydrogen bonds : bond 0.07524 / 4.89 ( 290) hydrogen bonds : angle 4.64254 / 3.25 ( 661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.218 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 41 average time/residue: 0.4434 time to fit residues: 19.8566 Evaluate side-chains 35 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 59 optimal weight: 30.0000 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 40.0000 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 50.0000 chunk 20 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.0173 > 50:) chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN A 355 HIS ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.106707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.083654 restraints weight = 37740.684| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.03 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8791 Z= 0.165 Angle : 0.675 12.598 12775 Z= 0.350 Chirality : 0.042 0.384 1557 Planarity : 0.005 0.050 955 Dihedral : 25.140 170.216 3465 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.79 % Allowed : 23.82 % Favored : 73.39 % 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: -2.46 (0.34), residues: 510 helix: 0.11 (0.43), residues: 148 sheet: -1.25 (0.58), residues: 71 loop : -2.83 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.033 0.002 TYR A 276 PHE 0.013 0.002 PHE B 184 TRP 0.077 0.005 TRP A 74 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 8791) covalent geometry : angle 0.67471 / 0.35 (12775) hydrogen bonds : bond 0.07412 / 4.81 ( 290) hydrogen bonds : angle 4.62032 / 3.22 ( 661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.192 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 41 average time/residue: 0.4179 time to fit residues: 18.8619 Evaluate side-chains 39 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 50.0000 chunk 25 optimal weight: 9.9990 chunk 61 optimal weight: 50.0000 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 30.0000 chunk 47 optimal weight: 0.0030 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.107854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.085289 restraints weight = 37470.855| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.02 r_work: 0.3910 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8791 Z= 0.134 Angle : 0.648 11.827 12775 Z= 0.337 Chirality : 0.041 0.382 1557 Planarity : 0.005 0.050 955 Dihedral : 25.079 170.296 3465 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.79 % Allowed : 23.61 % Favored : 73.61 % 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: -2.32 (0.34), residues: 510 helix: -0.00 (0.42), residues: 148 sheet: -1.01 (0.56), residues: 75 loop : -2.66 (0.32), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.028 0.002 TYR A 276 PHE 0.030 0.002 PHE B 124 TRP 0.087 0.005 TRP A 74 HIS 0.005 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 8791) covalent geometry : angle 0.64833 / 0.34 (12775) hydrogen bonds : bond 0.06871 / 4.52 ( 290) hydrogen bonds : angle 4.49997 / 3.13 ( 661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.202 Fit side-chains REVERT: A 209 MET cc_start: 0.4702 (mmp) cc_final: 0.4416 (mmt) REVERT: B 307 LYS cc_start: 0.6170 (mptt) cc_final: 0.4772 (mppt) outliers start: 13 outliers final: 8 residues processed: 43 average time/residue: 0.3832 time to fit residues: 18.1346 Evaluate side-chains 38 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN A 277 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.107325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.084733 restraints weight = 37960.219| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.01 r_work: 0.3899 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8791 Z= 0.155 Angle : 0.659 11.598 12775 Z= 0.343 Chirality : 0.042 0.386 1557 Planarity : 0.005 0.050 955 Dihedral : 25.066 170.522 3465 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.79 % Allowed : 23.82 % Favored : 73.39 % 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: -2.24 (0.34), residues: 510 helix: 0.19 (0.43), residues: 142 sheet: -0.98 (0.54), residues: 79 loop : -2.65 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.034 0.002 TYR A 276 PHE 0.025 0.002 PHE A 320 TRP 0.056 0.005 TRP A 74 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 8791) covalent geometry : angle 0.65941 / 0.34 (12775) hydrogen bonds : bond 0.07031 / 4.59 ( 290) hydrogen bonds : angle 4.50367 / 3.13 ( 661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2745.89 seconds wall clock time: 47 minutes 32.06 seconds (2852.06 seconds total)