Starting phenix.real_space_refine on Tue Feb 11 23:37:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ss5_25404/02_2025/7ss5_25404.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ss5_25404/02_2025/7ss5_25404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ss5_25404/02_2025/7ss5_25404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ss5_25404/02_2025/7ss5_25404.map" model { file = "/net/cci-nas-00/data/ceres_data/7ss5_25404/02_2025/7ss5_25404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ss5_25404/02_2025/7ss5_25404.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 48 5.49 5 S 18 5.16 5 C 3844 2.51 5 N 1140 2.21 5 O 1871 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6927 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 492 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 254 Classifications: {'water': 254} Link IDs: {None: 253} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "B" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Restraints were copied for chains: B, D Time building chain proxies: 5.67, per 1000 atoms: 0.82 Number of scatterers: 6927 At special positions: 0 Unit cell: (83, 86.32, 106.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 18 16.00 P 48 15.00 O 1871 8.00 N 1140 7.00 C 3844 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: 1.77 Conformation dependent library (CDL) restraints added in 622.9 milliseconds 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 51.8% alpha, 8.3% beta 18 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.653A pdb=" N ARG A 18 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 90 through 123 Processing helix chain 'A' and resid 161 through 178 removed outlier: 4.050A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.983A pdb=" N TRP A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 221 through 226 removed outlier: 4.029A pdb=" N ARG A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 226' Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.015A pdb=" N LEU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.653A pdb=" N ARG B 18 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 90 through 123 Processing helix chain 'B' and resid 161 through 178 removed outlier: 4.049A pdb=" N VAL B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.983A pdb=" N TRP B 204 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.028A pdb=" N ARG B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.015A pdb=" N LEU B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 149 removed outlier: 6.822A pdb=" N VAL A 193 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 235 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU A 276 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA A 238 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS A 278 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 240 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N LEU A 280 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N LYS A 242 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N TYR A 314 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 277 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 149 removed outlier: 6.822A pdb=" N VAL B 193 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 235 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N GLU B 276 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 238 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS B 278 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 240 " --> pdb=" O HIS B 278 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N LEU B 280 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N LYS B 242 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N TYR B 314 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 226 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.02 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: 1665 1.33 - 1.45: 1397 1.45 - 1.57: 3376 1.57 - 1.69: 94 1.69 - 1.81: 32 Bond restraints: 6564 Sorted by residual: bond pdb=" CA LEU A 296 " pdb=" C LEU A 296 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.10e-02 8.26e+03 2.44e+00 bond pdb=" CD ARG A 303 " pdb=" NE ARG A 303 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.40e+00 bond pdb=" CA LEU B 296 " pdb=" C LEU B 296 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.10e-02 8.26e+03 2.39e+00 bond pdb=" CD ARG B 303 " pdb=" NE ARG B 303 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.40e-02 5.10e+03 2.33e+00 bond pdb=" CA TYR B 297 " pdb=" C TYR B 297 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.10e-02 8.26e+03 2.08e+00 ... (remaining 6559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8853 1.56 - 3.11: 197 3.11 - 4.67: 40 4.67 - 6.22: 16 6.22 - 7.78: 4 Bond angle restraints: 9110 Sorted by residual: angle pdb=" N GLU A 292 " pdb=" CA GLU A 292 " pdb=" C GLU A 292 " ideal model delta sigma weight residual 110.68 102.90 7.78 1.39e+00 5.18e-01 3.13e+01 angle pdb=" N GLU B 292 " pdb=" CA GLU B 292 " pdb=" C GLU B 292 " ideal model delta sigma weight residual 110.68 102.94 7.74 1.39e+00 5.18e-01 3.10e+01 angle pdb=" N ARG A 311 " pdb=" CA ARG A 311 " pdb=" C ARG A 311 " ideal model delta sigma weight residual 111.28 117.33 -6.05 1.09e+00 8.42e-01 3.08e+01 angle pdb=" N ARG B 311 " pdb=" CA ARG B 311 " pdb=" C ARG B 311 " ideal model delta sigma weight residual 111.28 117.31 -6.03 1.09e+00 8.42e-01 3.06e+01 angle pdb=" N GLY B 58 " pdb=" CA GLY B 58 " pdb=" C GLY B 58 " ideal model delta sigma weight residual 112.73 107.77 4.96 1.20e+00 6.94e-01 1.71e+01 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 3547 34.80 - 69.60: 261 69.60 - 104.40: 6 104.40 - 139.20: 0 139.20 - 174.00: 2 Dihedral angle restraints: 3816 sinusoidal: 1858 harmonic: 1958 Sorted by residual: dihedral pdb=" C ALA B 55 " pdb=" N ALA B 55 " pdb=" CA ALA B 55 " pdb=" CB ALA B 55 " ideal model delta harmonic sigma weight residual -122.60 -111.34 -11.26 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C ALA A 55 " pdb=" N ALA A 55 " pdb=" CA ALA A 55 " pdb=" CB ALA A 55 " ideal model delta harmonic sigma weight residual -122.60 -111.36 -11.24 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CA GLN B 129 " pdb=" C GLN B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 913 0.077 - 0.155: 83 0.155 - 0.232: 4 0.232 - 0.309: 0 0.309 - 0.386: 2 Chirality restraints: 1002 Sorted by residual: chirality pdb=" CA ALA B 55 " pdb=" N ALA B 55 " pdb=" C ALA B 55 " pdb=" CB ALA B 55 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA ALA A 55 " pdb=" N ALA A 55 " pdb=" C ALA A 55 " pdb=" CB ALA A 55 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA GLU B 292 " pdb=" N GLU B 292 " pdb=" C GLU B 292 " pdb=" CB GLU B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 999 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 55 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C ALA B 55 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA B 55 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 56 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 55 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C ALA A 55 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA A 55 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 56 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 155 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ASP A 155 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP A 155 " -0.009 2.00e-02 2.50e+03 pdb=" N TRP A 156 " -0.008 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 441 2.72 - 3.27: 6424 3.27 - 3.81: 12394 3.81 - 4.36: 16446 4.36 - 4.90: 24478 Nonbonded interactions: 60183 Sorted by model distance: nonbonded pdb=" CG GLU A 301 " pdb=" CG GLU B 301 " model vdw 2.179 3.840 nonbonded pdb=" CA GLY B 266 " pdb=" OH TYR B 297 " model vdw 2.241 3.440 nonbonded pdb=" CA GLY A 266 " pdb=" OH TYR A 297 " model vdw 2.242 3.440 nonbonded pdb=" O HOH B 553 " pdb=" O HOH B 666 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASN B 92 " pdb=" O HOH B 501 " model vdw 2.287 3.040 ... (remaining 60178 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.660 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.990 Find NCS groups from input model: 0.150 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:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 0.035 6564 Z= 0.191 Angle : 0.633 7.778 9110 Z= 0.381 Chirality : 0.046 0.386 1002 Planarity : 0.004 0.033 1032 Dihedral : 19.806 173.997 2552 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.34), residues: 672 helix: 1.32 (0.34), residues: 280 sheet: -0.62 (0.74), residues: 50 loop : 0.09 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 156 HIS 0.002 0.001 HIS A 81 PHE 0.021 0.001 PHE A 171 TYR 0.014 0.001 TYR A 64 ARG 0.001 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.638 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 1.6979 time to fit residues: 271.6916 Evaluate side-chains 88 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 129 GLN A 307 HIS B 112 ASN B 227 GLN B 307 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.083482 restraints weight = 12288.017| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.49 r_work: 0.2889 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6564 Z= 0.343 Angle : 0.657 7.556 9110 Z= 0.346 Chirality : 0.043 0.135 1002 Planarity : 0.004 0.036 1032 Dihedral : 22.334 171.802 1270 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.13 % Allowed : 12.77 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.34), residues: 672 helix: 1.83 (0.33), residues: 292 sheet: -0.42 (0.73), residues: 50 loop : 0.12 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 PHE 0.011 0.001 PHE A 54 TYR 0.014 0.002 TYR A 5 ARG 0.006 0.001 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.733 Fit side-chains REVERT: A 256 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7718 (mt-10) REVERT: B 129 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8883 (tp40) outliers start: 12 outliers final: 5 residues processed: 97 average time/residue: 1.5428 time to fit residues: 156.5875 Evaluate side-chains 84 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 220 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.085701 restraints weight = 12090.814| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.52 r_work: 0.2914 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6564 Z= 0.251 Angle : 0.588 9.556 9110 Z= 0.307 Chirality : 0.041 0.126 1002 Planarity : 0.004 0.041 1032 Dihedral : 22.200 168.970 1270 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.30 % Allowed : 15.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.34), residues: 672 helix: 2.03 (0.32), residues: 292 sheet: -0.13 (0.72), residues: 48 loop : 0.26 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 156 HIS 0.002 0.001 HIS B 278 PHE 0.008 0.001 PHE B 54 TYR 0.013 0.002 TYR B 297 ARG 0.010 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.689 Fit side-chains REVERT: A 202 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 205 ARG cc_start: 0.8720 (mtp180) cc_final: 0.8478 (mtt180) outliers start: 13 outliers final: 5 residues processed: 94 average time/residue: 1.6596 time to fit residues: 162.6286 Evaluate side-chains 86 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 0.0670 chunk 31 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.084987 restraints weight = 12249.651| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.52 r_work: 0.2902 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6564 Z= 0.284 Angle : 0.591 7.580 9110 Z= 0.310 Chirality : 0.042 0.125 1002 Planarity : 0.004 0.034 1032 Dihedral : 22.388 169.115 1270 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.95 % Allowed : 16.67 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.35), residues: 672 helix: 2.16 (0.32), residues: 292 sheet: 0.04 (0.72), residues: 48 loop : 0.37 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 PHE 0.008 0.001 PHE B 54 TYR 0.011 0.002 TYR A 5 ARG 0.006 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.662 Fit side-chains REVERT: A 63 ASP cc_start: 0.8802 (t0) cc_final: 0.8299 (t0) REVERT: A 224 GLN cc_start: 0.9365 (mm-40) cc_final: 0.9146 (mp10) REVERT: B 121 MET cc_start: 0.9090 (mmp) cc_final: 0.8846 (mmm) outliers start: 11 outliers final: 5 residues processed: 97 average time/residue: 1.5223 time to fit residues: 154.5046 Evaluate side-chains 83 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 335 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086413 restraints weight = 12073.578| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.50 r_work: 0.2935 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6564 Z= 0.234 Angle : 0.570 6.639 9110 Z= 0.299 Chirality : 0.041 0.130 1002 Planarity : 0.004 0.025 1032 Dihedral : 22.345 169.380 1270 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.77 % Allowed : 18.09 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.35), residues: 672 helix: 2.29 (0.32), residues: 292 sheet: -0.15 (0.68), residues: 52 loop : 0.35 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 PHE 0.007 0.001 PHE B 54 TYR 0.012 0.002 TYR A 223 ARG 0.008 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.749 Fit side-chains REVERT: A 176 ARG cc_start: 0.8782 (tpp-160) cc_final: 0.8492 (tpp-160) REVERT: A 224 GLN cc_start: 0.9341 (mt0) cc_final: 0.9081 (mp10) REVERT: B 314 TYR cc_start: 0.9041 (t80) cc_final: 0.8816 (t80) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 1.7167 time to fit residues: 164.6859 Evaluate side-chains 87 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.110357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.085282 restraints weight = 12255.203| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.51 r_work: 0.2945 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 6564 Z= 0.382 Angle : 0.635 8.370 9110 Z= 0.336 Chirality : 0.044 0.129 1002 Planarity : 0.004 0.048 1032 Dihedral : 22.585 171.735 1270 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.30 % Allowed : 17.91 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.34), residues: 672 helix: 2.10 (0.32), residues: 292 sheet: -0.19 (0.66), residues: 52 loop : 0.29 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 156 HIS 0.002 0.001 HIS A 307 PHE 0.009 0.001 PHE B 54 TYR 0.017 0.002 TYR A 5 ARG 0.010 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.732 Fit side-chains REVERT: A 63 ASP cc_start: 0.8857 (t0) cc_final: 0.8342 (t0) REVERT: A 91 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8631 (p) REVERT: A 176 ARG cc_start: 0.8795 (tpp-160) cc_final: 0.8524 (tpp-160) REVERT: A 321 ASP cc_start: 0.9332 (t0) cc_final: 0.8845 (t0) REVERT: B 121 MET cc_start: 0.9124 (mmp) cc_final: 0.8883 (mmm) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 1.5327 time to fit residues: 139.8085 Evaluate side-chains 76 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 10.0000 chunk 52 optimal weight: 0.0770 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086165 restraints weight = 12112.273| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.46 r_work: 0.2959 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 6564 Z= 0.465 Angle : 0.667 7.319 9110 Z= 0.354 Chirality : 0.046 0.141 1002 Planarity : 0.004 0.056 1032 Dihedral : 22.645 170.057 1270 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.19 % Allowed : 17.02 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.34), residues: 672 helix: 1.95 (0.32), residues: 294 sheet: -0.29 (0.65), residues: 52 loop : 0.23 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 156 HIS 0.002 0.001 HIS A 81 PHE 0.009 0.001 PHE B 54 TYR 0.018 0.002 TYR A 5 ARG 0.008 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.743 Fit side-chains REVERT: A 91 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8530 (p) REVERT: A 176 ARG cc_start: 0.8783 (tpp-160) cc_final: 0.8493 (tpp-160) REVERT: A 224 GLN cc_start: 0.9329 (mm-40) cc_final: 0.9047 (mp10) REVERT: B 63 ASP cc_start: 0.8920 (t0) cc_final: 0.8610 (t0) REVERT: B 121 MET cc_start: 0.9123 (mmp) cc_final: 0.8897 (mmm) REVERT: B 314 TYR cc_start: 0.9115 (t80) cc_final: 0.8761 (t80) REVERT: B 335 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.8775 (tp30) outliers start: 18 outliers final: 9 residues processed: 89 average time/residue: 1.4392 time to fit residues: 134.5228 Evaluate side-chains 79 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 335 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 34 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088618 restraints weight = 12225.476| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.58 r_work: 0.3002 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6564 Z= 0.203 Angle : 0.590 6.961 9110 Z= 0.311 Chirality : 0.041 0.136 1002 Planarity : 0.004 0.035 1032 Dihedral : 22.473 170.309 1270 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.89 % Allowed : 19.50 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.35), residues: 672 helix: 2.26 (0.32), residues: 292 sheet: -0.33 (0.64), residues: 52 loop : 0.39 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 156 HIS 0.002 0.000 HIS A 81 PHE 0.008 0.001 PHE B 54 TYR 0.012 0.001 TYR B 297 ARG 0.010 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.701 Fit side-chains REVERT: A 166 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8663 (mm-30) REVERT: A 176 ARG cc_start: 0.8765 (tpp-160) cc_final: 0.8475 (tpp-160) REVERT: A 224 GLN cc_start: 0.9272 (mm-40) cc_final: 0.9021 (mp10) REVERT: B 121 MET cc_start: 0.9061 (mmp) cc_final: 0.8801 (mmm) outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 1.5221 time to fit residues: 123.0404 Evaluate side-chains 72 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.089475 restraints weight = 12215.546| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.53 r_work: 0.2942 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6564 Z= 0.263 Angle : 0.602 8.952 9110 Z= 0.315 Chirality : 0.042 0.132 1002 Planarity : 0.004 0.029 1032 Dihedral : 22.577 171.066 1270 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.89 % Allowed : 19.50 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.35), residues: 672 helix: 2.38 (0.32), residues: 290 sheet: -0.31 (0.64), residues: 52 loop : 0.38 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 156 HIS 0.002 0.001 HIS A 278 PHE 0.007 0.001 PHE B 54 TYR 0.020 0.002 TYR B 5 ARG 0.010 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.725 Fit side-chains REVERT: A 63 ASP cc_start: 0.8767 (t0) cc_final: 0.8224 (t0) REVERT: A 166 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8687 (mm-30) REVERT: A 176 ARG cc_start: 0.8763 (tpp-160) cc_final: 0.8464 (tpp-160) REVERT: A 224 GLN cc_start: 0.9349 (mm-40) cc_final: 0.9029 (mp10) REVERT: A 321 ASP cc_start: 0.9267 (t0) cc_final: 0.8899 (t0) REVERT: B 121 MET cc_start: 0.9051 (mmp) cc_final: 0.8846 (mmm) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 1.3910 time to fit residues: 112.8915 Evaluate side-chains 70 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 220 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.094525 restraints weight = 12201.038| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.54 r_work: 0.3102 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6564 Z= 0.176 Angle : 0.590 8.717 9110 Z= 0.305 Chirality : 0.040 0.128 1002 Planarity : 0.003 0.029 1032 Dihedral : 22.419 170.514 1270 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.71 % Allowed : 20.39 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.35), residues: 672 helix: 2.56 (0.32), residues: 290 sheet: -0.16 (0.68), residues: 48 loop : 0.52 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 156 HIS 0.001 0.000 HIS A 278 PHE 0.008 0.001 PHE B 54 TYR 0.013 0.001 TYR B 297 ARG 0.007 0.000 ARG B 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.708 Fit side-chains REVERT: A 63 ASP cc_start: 0.8692 (t0) cc_final: 0.8166 (t0) REVERT: A 166 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8702 (mm-30) REVERT: A 176 ARG cc_start: 0.8786 (tpp-160) cc_final: 0.8476 (tpp-160) REVERT: A 224 GLN cc_start: 0.9318 (mm-40) cc_final: 0.9036 (mp10) REVERT: A 321 ASP cc_start: 0.9158 (t0) cc_final: 0.8808 (t0) REVERT: B 121 MET cc_start: 0.9004 (mmp) cc_final: 0.8771 (mmm) outliers start: 4 outliers final: 4 residues processed: 82 average time/residue: 1.3157 time to fit residues: 114.0177 Evaluate side-chains 82 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.089433 restraints weight = 11996.713| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.51 r_work: 0.2962 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6564 Z= 0.275 Angle : 0.606 8.467 9110 Z= 0.318 Chirality : 0.042 0.129 1002 Planarity : 0.004 0.030 1032 Dihedral : 22.595 173.198 1270 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.71 % Allowed : 20.74 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.35), residues: 672 helix: 2.52 (0.32), residues: 290 sheet: -0.31 (0.66), residues: 52 loop : 0.39 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 PHE 0.007 0.001 PHE B 54 TYR 0.019 0.002 TYR B 5 ARG 0.007 0.000 ARG B 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5240.74 seconds wall clock time: 92 minutes 46.12 seconds (5566.12 seconds total)