Starting phenix.real_space_refine on Tue Mar 11 23:12:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ss5_25404/03_2025/7ss5_25404.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ss5_25404/03_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_25404/03_2025/7ss5_25404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ss5_25404/03_2025/7ss5_25404.map" model { file = "/net/cci-nas-00/data/ceres_data/7ss5_25404/03_2025/7ss5_25404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ss5_25404/03_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.38, per 1000 atoms: 0.92 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: 2.03 Conformation dependent library (CDL) restraints added in 689.1 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: 2.72 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: 2.38 Time building geometry restraints manager: 2.26 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: 1.420 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: 0.080 Process input model: 23.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- 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 : 0.725 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 1.6639 time to fit residues: 266.2601 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 : 0.718 ------------------------------------------------------------------------------- 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 = 0.108280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.083991 restraints weight = 12211.251| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.52 r_work: 0.2887 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 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 : 0.703 Fit side-chains REVERT: A 256 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7722 (mt-10) REVERT: B 129 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8880 (tp40) outliers start: 12 outliers final: 5 residues processed: 97 average time/residue: 1.5696 time to fit residues: 159.0488 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 : 0.729 ------------------------------------------------------------------------------- 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: 1.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.111231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086430 restraints weight = 12027.253| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.55 r_work: 0.2928 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6564 Z= 0.218 Angle : 0.575 9.214 9110 Z= 0.300 Chirality : 0.041 0.126 1002 Planarity : 0.004 0.041 1032 Dihedral : 22.141 168.689 1270 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.13 % Allowed : 15.07 % Favored : 82.80 % 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: 1.48 (0.34), residues: 672 helix: 2.05 (0.32), residues: 292 sheet: -0.11 (0.72), residues: 48 loop : 0.27 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 156 HIS 0.001 0.001 HIS B 278 PHE 0.008 0.001 PHE B 54 TYR 0.013 0.001 TYR B 297 ARG 0.008 0.000 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 100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.665 Fit side-chains REVERT: A 202 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 205 ARG cc_start: 0.8718 (mtp180) cc_final: 0.8476 (mtt180) REVERT: B 260 MET cc_start: 0.9169 (mtp) cc_final: 0.8857 (mmt) REVERT: B 314 TYR cc_start: 0.9047 (t80) cc_final: 0.8761 (t80) outliers start: 12 outliers final: 5 residues processed: 94 average time/residue: 1.5894 time to fit residues: 155.7822 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 : 0.727 ------------------------------------------------------------------------------- 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: 8.9990 chunk 31 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.083570 restraints weight = 12278.496| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.54 r_work: 0.2864 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 6564 Z= 0.406 Angle : 0.637 6.996 9110 Z= 0.338 Chirality : 0.044 0.133 1002 Planarity : 0.004 0.051 1032 Dihedral : 22.539 169.961 1270 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.95 % Allowed : 17.38 % Favored : 80.67 % 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: 1.40 (0.34), residues: 672 helix: 2.01 (0.32), residues: 292 sheet: -0.15 (0.68), residues: 52 loop : 0.21 (0.37), residues: 328 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 0.009 0.001 PHE B 54 TYR 0.018 0.002 TYR A 5 ARG 0.008 0.001 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 95 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.667 Fit side-chains REVERT: A 63 ASP cc_start: 0.8867 (t0) cc_final: 0.8359 (t0) REVERT: B 36 GLN cc_start: 0.9057 (tt0) cc_final: 0.8843 (tt0) REVERT: B 252 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 256 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8043 (mt-10) outliers start: 11 outliers final: 4 residues processed: 91 average time/residue: 1.4059 time to fit residues: 134.1633 Evaluate side-chains 80 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 85 ASP 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 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.112209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.087296 restraints weight = 12120.233| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.56 r_work: 0.2969 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6564 Z= 0.182 Angle : 0.570 8.481 9110 Z= 0.297 Chirality : 0.040 0.126 1002 Planarity : 0.003 0.027 1032 Dihedral : 22.244 169.272 1270 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.24 % Allowed : 17.20 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.35), residues: 672 helix: 2.28 (0.32), residues: 292 sheet: -0.01 (0.72), residues: 48 loop : 0.39 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 PHE 0.008 0.001 PHE B 54 TYR 0.013 0.001 TYR B 297 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 97 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.752 Fit side-chains REVERT: A 63 ASP cc_start: 0.8712 (t0) cc_final: 0.8217 (t0) REVERT: B 36 GLN cc_start: 0.8929 (tt0) cc_final: 0.8389 (tt0) REVERT: B 314 TYR cc_start: 0.9048 (t80) cc_final: 0.8785 (t80) outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 1.5175 time to fit residues: 149.1266 Evaluate side-chains 74 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 64 TYR Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.085314 restraints weight = 12230.784| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.51 r_work: 0.2902 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6564 Z= 0.328 Angle : 0.605 6.363 9110 Z= 0.321 Chirality : 0.043 0.125 1002 Planarity : 0.004 0.038 1032 Dihedral : 22.493 169.908 1270 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.60 % Allowed : 18.62 % 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: 1.53 (0.34), residues: 672 helix: 2.12 (0.32), residues: 294 sheet: -0.25 (0.65), residues: 52 loop : 0.30 (0.38), residues: 326 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 0.008 0.001 PHE B 54 TYR 0.023 0.002 TYR B 5 ARG 0.009 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 83 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.716 Fit side-chains REVERT: A 91 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 36 GLN cc_start: 0.9000 (tt0) cc_final: 0.8563 (tt0) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 1.5771 time to fit residues: 130.2717 Evaluate side-chains 74 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 85 ASP Chi-restraints excluded: chain B residue 167 VAL 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: 8.9990 chunk 52 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 overall best weight: 5.4106 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.111092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086502 restraints weight = 12067.385| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.45 r_work: 0.2936 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 6564 Z= 0.408 Angle : 0.653 9.275 9110 Z= 0.344 Chirality : 0.045 0.128 1002 Planarity : 0.004 0.047 1032 Dihedral : 22.584 170.675 1270 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.48 % Allowed : 17.38 % 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: 1.41 (0.34), residues: 672 helix: 2.00 (0.32), residues: 294 sheet: -0.33 (0.63), residues: 52 loop : 0.25 (0.38), residues: 326 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 0.009 0.001 PHE A 275 TYR 0.026 0.002 TYR B 5 ARG 0.010 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 87 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.766 Fit side-chains REVERT: A 224 GLN cc_start: 0.9305 (mm-40) cc_final: 0.9023 (mp10) REVERT: B 36 GLN cc_start: 0.9026 (tt0) cc_final: 0.8800 (tt0) REVERT: B 314 TYR cc_start: 0.9098 (t80) cc_final: 0.8775 (t80) outliers start: 14 outliers final: 8 residues processed: 83 average time/residue: 1.3866 time to fit residues: 120.8926 Evaluate side-chains 72 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 0.0030 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 0.0170 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.1832 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.113564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087748 restraints weight = 12132.501| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.58 r_work: 0.3019 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3941 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= 0.220 Angle : 0.585 7.067 9110 Z= 0.308 Chirality : 0.041 0.127 1002 Planarity : 0.004 0.035 1032 Dihedral : 22.488 169.953 1270 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.60 % Allowed : 18.97 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.34), residues: 672 helix: 2.27 (0.32), residues: 292 sheet: -0.43 (0.63), residues: 52 loop : 0.39 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 156 HIS 0.001 0.001 HIS A 81 PHE 0.008 0.001 PHE B 54 TYR 0.016 0.001 TYR B 5 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: 9 poor density : 70 time to evaluate : 0.682 Fit side-chains REVERT: A 224 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9023 (mp10) REVERT: B 36 GLN cc_start: 0.8968 (tt0) cc_final: 0.8458 (tt0) REVERT: B 311 ARG cc_start: 0.9265 (ttp80) cc_final: 0.8918 (mtp85) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 1.3684 time to fit residues: 109.3191 Evaluate side-chains 76 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 167 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 263 LEU 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: 8.9990 chunk 46 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.111610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.086383 restraints weight = 12303.642| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.47 r_work: 0.2953 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 6564 Z= 0.386 Angle : 0.651 9.158 9110 Z= 0.343 Chirality : 0.044 0.126 1002 Planarity : 0.004 0.043 1032 Dihedral : 22.660 171.033 1270 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.60 % Allowed : 18.44 % Favored : 79.96 % 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: 1.51 (0.34), residues: 672 helix: 2.11 (0.32), residues: 294 sheet: -0.34 (0.63), residues: 52 loop : 0.29 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 156 HIS 0.002 0.001 HIS A 81 PHE 0.008 0.001 PHE B 54 TYR 0.028 0.002 TYR B 5 ARG 0.011 0.001 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 81 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.704 Fit side-chains REVERT: A 63 ASP cc_start: 0.8818 (t0) cc_final: 0.8283 (t0) REVERT: A 91 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8504 (p) REVERT: A 166 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8658 (mm-30) REVERT: A 203 MET cc_start: 0.9384 (ppp) cc_final: 0.9099 (ppp) REVERT: A 224 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8986 (mp10) REVERT: A 321 ASP cc_start: 0.9328 (t0) cc_final: 0.8877 (t0) REVERT: B 36 GLN cc_start: 0.9039 (tt0) cc_final: 0.8825 (tt0) REVERT: B 121 MET cc_start: 0.9084 (mmp) cc_final: 0.8837 (mmm) REVERT: B 314 TYR cc_start: 0.9036 (t80) cc_final: 0.8802 (t80) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 1.3017 time to fit residues: 108.4035 Evaluate side-chains 74 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 167 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 263 LEU 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: 9.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.0670 chunk 32 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.116224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.091175 restraints weight = 12351.679| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.52 r_work: 0.3024 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6564 Z= 0.179 Angle : 0.588 8.818 9110 Z= 0.305 Chirality : 0.040 0.127 1002 Planarity : 0.003 0.028 1032 Dihedral : 22.437 170.551 1270 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.24 % Allowed : 19.15 % 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: 1.90 (0.35), residues: 672 helix: 2.46 (0.32), residues: 292 sheet: -0.19 (0.66), residues: 48 loop : 0.49 (0.38), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 156 HIS 0.001 0.001 HIS A 81 PHE 0.009 0.001 PHE B 54 TYR 0.013 0.001 TYR B 297 ARG 0.006 0.000 ARG B 65 ********************** 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 94 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.686 Fit side-chains REVERT: A 63 ASP cc_start: 0.8711 (t0) cc_final: 0.8170 (t0) REVERT: A 166 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8693 (mm-30) REVERT: A 224 GLN cc_start: 0.9287 (mm-40) cc_final: 0.8994 (mp10) REVERT: A 248 ASP cc_start: 0.9315 (p0) cc_final: 0.9106 (p0) REVERT: A 321 ASP cc_start: 0.9184 (t0) cc_final: 0.8816 (t0) REVERT: B 36 GLN cc_start: 0.8911 (tt0) cc_final: 0.8373 (tt0) REVERT: B 201 ASP cc_start: 0.8835 (t0) cc_final: 0.8602 (t0) REVERT: B 311 ARG cc_start: 0.9214 (ttp80) cc_final: 0.8911 (mtp85) REVERT: B 314 TYR cc_start: 0.8968 (t80) cc_final: 0.8750 (t80) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 1.2685 time to fit residues: 123.2925 Evaluate side-chains 82 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 167 VAL Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 49 optimal weight: 9.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.114210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088836 restraints weight = 12228.005| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.51 r_work: 0.2972 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4150 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= 0.273 Angle : 0.608 7.119 9110 Z= 0.321 Chirality : 0.042 0.126 1002 Planarity : 0.004 0.034 1032 Dihedral : 22.539 171.033 1270 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.24 % Allowed : 19.33 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.35), residues: 672 helix: 2.41 (0.32), residues: 292 sheet: -0.44 (0.63), residues: 52 loop : 0.35 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 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 0.007 0.000 ARG B 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5242.86 seconds wall clock time: 89 minutes 44.44 seconds (5384.44 seconds total)