Starting phenix.real_space_refine on Wed Sep 17 06:40:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgj_44514/09_2025/9bgj_44514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgj_44514/09_2025/9bgj_44514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bgj_44514/09_2025/9bgj_44514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgj_44514/09_2025/9bgj_44514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bgj_44514/09_2025/9bgj_44514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgj_44514/09_2025/9bgj_44514.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.069 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 P 50 5.49 5 Mg 2 5.21 5 S 18 5.16 5 C 3849 2.51 5 N 1145 2.21 5 O 1297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6361 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2669 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: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 517 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "B" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2640 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 19, 'TRANS': 314} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 524 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.78, per 1000 atoms: 0.28 Number of scatterers: 6361 At special positions: 0 Unit cell: (82.17, 83.83, 100.43, 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) S 18 16.00 P 50 15.00 Mg 2 11.99 O 1297 8.00 N 1145 7.00 C 3849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 276.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1258 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 51.0% alpha, 6.0% beta 19 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.643A pdb=" N ARG A 18 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.528A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) 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 removed outlier: 3.912A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 143 Processing helix chain 'A' and resid 161 through 177 removed outlier: 4.595A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.556A pdb=" N ARG A 205 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 206 " --> pdb=" O MET A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 206' Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.835A pdb=" N ARG A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.982A pdb=" N ILE A 235 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.680A pdb=" N LEU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.854A pdb=" N LEU A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.744A pdb=" N ARG B 18 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.526A pdb=" N GLY B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) 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 removed outlier: 3.941A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 143 Processing helix chain 'B' and resid 161 through 177 removed outlier: 5.264A pdb=" N VAL B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.259A pdb=" N ARG B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.205A 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: 3.726A pdb=" N LEU B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.891A pdb=" N LEU B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) 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 148 removed outlier: 6.316A pdb=" N ALA A 238 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N HIS A 278 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA A 240 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TYR A 314 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.749A 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 148 removed outlier: 6.777A pdb=" N VAL B 193 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 235 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLU B 276 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA B 238 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS B 278 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 240 " --> pdb=" O HIS B 278 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N TYR B 314 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.75 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: 1687 1.33 - 1.45: 1379 1.45 - 1.57: 3395 1.57 - 1.69: 99 1.69 - 1.80: 32 Bond restraints: 6592 Sorted by residual: bond pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.23e-02 6.61e+03 3.39e+00 bond pdb=" N ASP B 63 " pdb=" CA ASP B 63 " ideal model delta sigma weight residual 1.456 1.477 -0.021 1.23e-02 6.61e+03 2.97e+00 bond pdb=" C3' DT C 24 " pdb=" O3' DT C 24 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" C ASP B 63 " pdb=" N TYR B 64 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.38e-02 5.25e+03 1.35e+00 bond pdb=" C ASP A 63 " pdb=" N TYR A 64 " ideal model delta sigma weight residual 1.335 1.322 0.014 1.38e-02 5.25e+03 9.63e-01 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 8755 1.10 - 2.20: 309 2.20 - 3.29: 66 3.29 - 4.39: 18 4.39 - 5.49: 12 Bond angle restraints: 9160 Sorted by residual: angle pdb=" N VAL B 157 " pdb=" CA VAL B 157 " pdb=" C VAL B 157 " ideal model delta sigma weight residual 113.39 108.20 5.19 1.47e+00 4.63e-01 1.25e+01 angle pdb=" N ASP A 85 " pdb=" CA ASP A 85 " pdb=" C ASP A 85 " ideal model delta sigma weight residual 113.72 108.46 5.26 1.52e+00 4.33e-01 1.20e+01 angle pdb=" N VAL B 28 " pdb=" CA VAL B 28 " pdb=" C VAL B 28 " ideal model delta sigma weight residual 110.21 106.45 3.76 1.13e+00 7.83e-01 1.11e+01 angle pdb=" N ASP A 85 " pdb=" CA ASP A 85 " pdb=" CB ASP A 85 " ideal model delta sigma weight residual 113.65 109.55 4.10 1.47e+00 4.63e-01 7.78e+00 angle pdb=" CA VAL B 157 " pdb=" C VAL B 157 " pdb=" N SER B 158 " ideal model delta sigma weight residual 118.55 116.48 2.07 8.60e-01 1.35e+00 5.78e+00 ... (remaining 9155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.21: 3028 19.21 - 38.41: 474 38.41 - 57.62: 273 57.62 - 76.82: 32 76.82 - 96.03: 11 Dihedral angle restraints: 3818 sinusoidal: 1871 harmonic: 1947 Sorted by residual: 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 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA GLN A 129 " pdb=" C GLN A 129 " pdb=" N PRO A 130 " pdb=" CA PRO A 130 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CG ARG B 308 " pdb=" CD ARG B 308 " pdb=" NE ARG B 308 " pdb=" CZ ARG B 308 " ideal model delta sinusoidal sigma weight residual -180.00 -135.52 -44.48 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 3815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 680 0.033 - 0.066: 231 0.066 - 0.099: 60 0.099 - 0.131: 35 0.131 - 0.164: 2 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA TYR A 297 " pdb=" N TYR A 297 " pdb=" C TYR A 297 " pdb=" CB TYR A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA VAL B 161 " pdb=" N VAL B 161 " pdb=" C VAL B 161 " pdb=" CB VAL B 161 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA PRO B 162 " pdb=" N PRO B 162 " pdb=" C PRO B 162 " pdb=" CB PRO B 162 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1005 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 85 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" CG ASP A 85 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 85 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 85 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 231 " 0.024 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO B 232 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 231 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 232 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.019 5.00e-02 4.00e+02 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 55 2.52 - 3.11: 4509 3.11 - 3.71: 10089 3.71 - 4.30: 14248 4.30 - 4.90: 23596 Nonbonded interactions: 52497 Sorted by model distance: nonbonded pdb=" OP1 DC D 12 " pdb="MG MG B 401 " model vdw 1.922 2.170 nonbonded pdb=" OP1 DC C 12 " pdb="MG MG A 401 " model vdw 1.925 2.170 nonbonded pdb=" O PHE B 241 " pdb="MG MG B 401 " model vdw 2.117 2.170 nonbonded pdb=" O PHE A 241 " pdb="MG MG A 401 " model vdw 2.182 2.170 nonbonded pdb=" OD2 ASP B 188 " pdb="MG MG B 401 " model vdw 2.216 2.170 ... (remaining 52492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 299 or resid 304 through 401)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.310 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 0.038 6592 Z= 0.148 Angle : 0.542 5.488 9160 Z= 0.300 Chirality : 0.040 0.164 1008 Planarity : 0.004 0.037 1028 Dihedral : 22.775 96.030 2560 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.93 % Allowed : 26.43 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.35), residues: 666 helix: 0.95 (0.33), residues: 282 sheet: -1.23 (0.73), residues: 43 loop : -0.78 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 225 TYR 0.017 0.001 TYR A 297 PHE 0.021 0.001 PHE B 171 TRP 0.011 0.001 TRP A 117 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6592) covalent geometry : angle 0.54153 ( 9160) hydrogen bonds : bond 0.15872 ( 264) hydrogen bonds : angle 5.41762 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.223 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 24 ARG cc_start: 0.6699 (tmt170) cc_final: 0.5822 (tpt-90) REVERT: A 103 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8099 (tt0) REVERT: A 196 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8514 (mm-30) REVERT: B 24 ARG cc_start: 0.6069 (tmt170) cc_final: 0.2271 (mtm180) REVERT: B 85 ASP cc_start: 0.7848 (t0) cc_final: 0.7435 (t0) REVERT: B 142 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7780 (mtp-110) REVERT: B 166 GLU cc_start: 0.7609 (tp30) cc_final: 0.7327 (mt-10) REVERT: B 202 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6892 (mp0) outliers start: 22 outliers final: 18 residues processed: 76 average time/residue: 0.0998 time to fit residues: 9.7567 Evaluate side-chains 80 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN B 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.161744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116856 restraints weight = 6583.031| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.95 r_work: 0.3167 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6592 Z= 0.192 Angle : 0.540 5.594 9160 Z= 0.287 Chirality : 0.041 0.168 1008 Planarity : 0.004 0.036 1028 Dihedral : 23.521 95.556 1325 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 6.43 % Allowed : 23.21 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.35), residues: 666 helix: 1.55 (0.33), residues: 267 sheet: -1.52 (0.71), residues: 44 loop : -0.48 (0.37), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.005 0.001 PHE B 87 TRP 0.012 0.002 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 6592) covalent geometry : angle 0.54042 ( 9160) hydrogen bonds : bond 0.04194 ( 264) hydrogen bonds : angle 3.88652 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 0.204 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6530 (tmt170) cc_final: 0.5737 (tpt-90) REVERT: A 103 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8126 (tt0) REVERT: A 124 GLU cc_start: 0.8295 (mp0) cc_final: 0.8094 (mp0) REVERT: B 24 ARG cc_start: 0.6145 (tmt170) cc_final: 0.2228 (mtm180) REVERT: B 85 ASP cc_start: 0.7875 (t0) cc_final: 0.7603 (t0) REVERT: B 166 GLU cc_start: 0.7563 (tp30) cc_final: 0.7244 (mt-10) REVERT: B 202 GLU cc_start: 0.7742 (mt-10) cc_final: 0.6956 (mp0) outliers start: 36 outliers final: 19 residues processed: 97 average time/residue: 0.0858 time to fit residues: 11.0575 Evaluate side-chains 80 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 289 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 30 optimal weight: 0.0470 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.161523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116434 restraints weight = 6570.706| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.96 r_work: 0.3160 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6592 Z= 0.195 Angle : 0.539 5.453 9160 Z= 0.284 Chirality : 0.041 0.169 1008 Planarity : 0.004 0.035 1028 Dihedral : 23.438 95.140 1306 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 6.79 % Allowed : 22.86 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.35), residues: 666 helix: 1.65 (0.33), residues: 267 sheet: -1.53 (0.72), residues: 44 loop : -0.48 (0.37), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.019 0.001 TYR A 297 PHE 0.005 0.001 PHE B 54 TRP 0.011 0.002 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 6592) covalent geometry : angle 0.53872 ( 9160) hydrogen bonds : bond 0.03972 ( 264) hydrogen bonds : angle 3.80235 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 67 time to evaluate : 0.169 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: A 24 ARG cc_start: 0.6507 (tmt170) cc_final: 0.5699 (tpt-90) REVERT: A 103 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8095 (tt0) REVERT: A 124 GLU cc_start: 0.8293 (mp0) cc_final: 0.8016 (mp0) REVERT: A 196 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8548 (mm-30) REVERT: B 24 ARG cc_start: 0.6052 (tmt170) cc_final: 0.2156 (mtm180) REVERT: B 85 ASP cc_start: 0.7884 (t0) cc_final: 0.7627 (t0) REVERT: B 142 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7981 (mtm180) REVERT: B 166 GLU cc_start: 0.7590 (tp30) cc_final: 0.7183 (mt-10) REVERT: B 202 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7050 (tp30) REVERT: B 260 MET cc_start: 0.8497 (ttt) cc_final: 0.8252 (ttt) outliers start: 38 outliers final: 22 residues processed: 96 average time/residue: 0.0942 time to fit residues: 11.6299 Evaluate side-chains 90 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 212 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.172911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127455 restraints weight = 6622.660| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.93 r_work: 0.3359 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6592 Z= 0.114 Angle : 0.488 5.693 9160 Z= 0.260 Chirality : 0.039 0.165 1008 Planarity : 0.003 0.032 1028 Dihedral : 22.999 95.340 1306 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.82 % Allowed : 24.64 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.35), residues: 666 helix: 1.94 (0.34), residues: 267 sheet: -1.34 (0.76), residues: 41 loop : -0.45 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.017 0.001 TYR A 297 PHE 0.007 0.001 PHE B 87 TRP 0.011 0.001 TRP A 117 HIS 0.000 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6592) covalent geometry : angle 0.48754 ( 9160) hydrogen bonds : bond 0.03062 ( 264) hydrogen bonds : angle 3.55180 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.203 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: A 24 ARG cc_start: 0.6449 (tmt170) cc_final: 0.5585 (tpt-90) REVERT: A 85 ASP cc_start: 0.7188 (t0) cc_final: 0.6966 (t0) REVERT: A 103 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8142 (tt0) REVERT: A 124 GLU cc_start: 0.8251 (mp0) cc_final: 0.7967 (mp0) REVERT: A 196 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8508 (mm-30) REVERT: B 17 GLU cc_start: 0.8094 (tt0) cc_final: 0.7800 (mt-10) REVERT: B 24 ARG cc_start: 0.6069 (tmt170) cc_final: 0.2124 (mtm180) REVERT: B 85 ASP cc_start: 0.7691 (t0) cc_final: 0.7358 (t0) REVERT: B 142 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7982 (mtm180) REVERT: B 166 GLU cc_start: 0.7657 (tp30) cc_final: 0.7241 (mt-10) REVERT: B 202 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7097 (tp30) REVERT: B 312 GLU cc_start: 0.8805 (tt0) cc_final: 0.8443 (tt0) outliers start: 27 outliers final: 16 residues processed: 87 average time/residue: 0.0995 time to fit residues: 11.1372 Evaluate side-chains 81 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG 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 18 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.173979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128595 restraints weight = 6716.820| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.97 r_work: 0.3374 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6592 Z= 0.110 Angle : 0.482 5.897 9160 Z= 0.254 Chirality : 0.039 0.167 1008 Planarity : 0.003 0.031 1028 Dihedral : 22.887 96.337 1305 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.00 % Allowed : 24.64 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.35), residues: 666 helix: 2.08 (0.34), residues: 267 sheet: -1.19 (0.77), residues: 41 loop : -0.45 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.017 0.001 TYR A 297 PHE 0.006 0.001 PHE B 87 TRP 0.013 0.001 TRP B 156 HIS 0.000 0.000 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6592) covalent geometry : angle 0.48212 ( 9160) hydrogen bonds : bond 0.02906 ( 264) hydrogen bonds : angle 3.44349 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.233 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: A 24 ARG cc_start: 0.6319 (tmt170) cc_final: 0.5451 (tpt-90) REVERT: A 29 ARG cc_start: 0.7895 (mmm-85) cc_final: 0.7642 (mmm-85) REVERT: A 85 ASP cc_start: 0.7143 (t0) cc_final: 0.6842 (t0) REVERT: A 86 ASP cc_start: 0.7927 (t0) cc_final: 0.7693 (t0) REVERT: A 103 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8086 (tt0) REVERT: A 124 GLU cc_start: 0.8202 (mp0) cc_final: 0.7897 (mp0) REVERT: A 196 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8529 (mm-30) REVERT: B 17 GLU cc_start: 0.8071 (tt0) cc_final: 0.7774 (mt-10) REVERT: B 24 ARG cc_start: 0.6039 (tmt170) cc_final: 0.2078 (mtm180) REVERT: B 85 ASP cc_start: 0.7732 (t0) cc_final: 0.7411 (t0) REVERT: B 142 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7955 (mtm180) REVERT: B 166 GLU cc_start: 0.7611 (tp30) cc_final: 0.7181 (mt-10) REVERT: B 202 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7091 (tp30) REVERT: B 312 GLU cc_start: 0.8755 (tt0) cc_final: 0.8380 (tt0) outliers start: 28 outliers final: 20 residues processed: 88 average time/residue: 0.0936 time to fit residues: 10.5423 Evaluate side-chains 88 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 0.0170 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.0050 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 overall best weight: 1.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127599 restraints weight = 6675.213| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.97 r_work: 0.3363 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6592 Z= 0.120 Angle : 0.483 5.822 9160 Z= 0.254 Chirality : 0.039 0.167 1008 Planarity : 0.003 0.030 1028 Dihedral : 22.918 97.542 1304 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.82 % Allowed : 23.93 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.36), residues: 666 helix: 2.10 (0.33), residues: 267 sheet: -0.94 (0.76), residues: 46 loop : -0.43 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.004 0.001 PHE B 87 TRP 0.010 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6592) covalent geometry : angle 0.48343 ( 9160) hydrogen bonds : bond 0.02954 ( 264) hydrogen bonds : angle 3.43246 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.229 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: A 24 ARG cc_start: 0.6356 (tmt170) cc_final: 0.5506 (tpt-90) REVERT: A 29 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7627 (mmm-85) REVERT: A 42 MET cc_start: 0.8533 (mtm) cc_final: 0.8300 (mtm) REVERT: A 85 ASP cc_start: 0.7178 (t0) cc_final: 0.6866 (t0) REVERT: A 86 ASP cc_start: 0.7953 (t0) cc_final: 0.7697 (t0) REVERT: A 103 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8107 (tt0) REVERT: A 124 GLU cc_start: 0.8179 (mp0) cc_final: 0.7926 (mp0) REVERT: A 196 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8588 (mm-30) REVERT: B 17 GLU cc_start: 0.8088 (tt0) cc_final: 0.7794 (mt-10) REVERT: B 24 ARG cc_start: 0.6034 (tmt170) cc_final: 0.2100 (mtm180) REVERT: B 85 ASP cc_start: 0.7715 (t0) cc_final: 0.7422 (t0) REVERT: B 142 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7944 (mtm180) REVERT: B 166 GLU cc_start: 0.7615 (tp30) cc_final: 0.7228 (mt-10) REVERT: B 312 GLU cc_start: 0.8799 (tt0) cc_final: 0.8426 (tt0) outliers start: 27 outliers final: 19 residues processed: 87 average time/residue: 0.1018 time to fit residues: 11.2565 Evaluate side-chains 85 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN B 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116294 restraints weight = 6674.091| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.92 r_work: 0.3157 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6592 Z= 0.221 Angle : 0.549 5.429 9160 Z= 0.287 Chirality : 0.042 0.167 1008 Planarity : 0.004 0.032 1028 Dihedral : 23.400 100.365 1304 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 5.54 % Allowed : 23.21 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.35), residues: 666 helix: 1.82 (0.33), residues: 267 sheet: -1.09 (0.76), residues: 46 loop : -0.44 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.006 0.001 PHE B 102 TRP 0.011 0.002 TRP B 156 HIS 0.001 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 6592) covalent geometry : angle 0.54891 ( 9160) hydrogen bonds : bond 0.03924 ( 264) hydrogen bonds : angle 3.65293 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.248 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: A 24 ARG cc_start: 0.6468 (tmt170) cc_final: 0.5648 (tpt-90) REVERT: A 103 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8102 (tt0) REVERT: A 124 GLU cc_start: 0.8054 (mp0) cc_final: 0.7652 (mp0) REVERT: A 196 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8595 (mm-30) REVERT: B 17 GLU cc_start: 0.8098 (tt0) cc_final: 0.7831 (mt-10) REVERT: B 24 ARG cc_start: 0.6053 (tmt170) cc_final: 0.2099 (mtm180) REVERT: B 142 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7927 (mtm180) REVERT: B 169 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7132 (tm-30) REVERT: B 312 GLU cc_start: 0.8761 (tt0) cc_final: 0.8376 (tt0) outliers start: 31 outliers final: 21 residues processed: 86 average time/residue: 0.1015 time to fit residues: 11.3625 Evaluate side-chains 84 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN B 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.166171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120566 restraints weight = 6543.904| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.01 r_work: 0.3220 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6592 Z= 0.124 Angle : 0.497 5.647 9160 Z= 0.263 Chirality : 0.039 0.167 1008 Planarity : 0.003 0.030 1028 Dihedral : 23.007 100.643 1304 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.71 % Allowed : 23.21 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.35), residues: 666 helix: 2.04 (0.33), residues: 267 sheet: -0.98 (0.77), residues: 46 loop : -0.39 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.017 0.001 TYR A 297 PHE 0.005 0.001 PHE B 87 TRP 0.010 0.001 TRP A 117 HIS 0.000 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6592) covalent geometry : angle 0.49710 ( 9160) hydrogen bonds : bond 0.03107 ( 264) hydrogen bonds : angle 3.48596 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.228 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: A 24 ARG cc_start: 0.6296 (tmt170) cc_final: 0.5460 (tpt-90) REVERT: A 103 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8078 (tt0) REVERT: A 124 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: A 142 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8013 (mtm180) REVERT: A 196 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8615 (mm-30) REVERT: B 17 GLU cc_start: 0.8077 (tt0) cc_final: 0.7786 (mt-10) REVERT: B 24 ARG cc_start: 0.5876 (tmt170) cc_final: 0.1974 (mtm180) REVERT: B 85 ASP cc_start: 0.7754 (t0) cc_final: 0.7549 (t0) REVERT: B 142 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7885 (mtm180) REVERT: B 169 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7069 (tm-30) REVERT: B 202 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7138 (tp30) REVERT: B 225 ARG cc_start: 0.8523 (mtt90) cc_final: 0.8244 (mtt90) REVERT: B 312 GLU cc_start: 0.8811 (tt0) cc_final: 0.8452 (tt0) outliers start: 32 outliers final: 21 residues processed: 87 average time/residue: 0.1068 time to fit residues: 11.9084 Evaluate side-chains 89 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119167 restraints weight = 6700.837| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.97 r_work: 0.3197 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6592 Z= 0.160 Angle : 0.509 5.607 9160 Z= 0.269 Chirality : 0.040 0.169 1008 Planarity : 0.004 0.031 1028 Dihedral : 23.075 102.415 1304 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 5.89 % Allowed : 22.68 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.35), residues: 666 helix: 1.96 (0.33), residues: 267 sheet: -0.94 (0.77), residues: 46 loop : -0.42 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.017 0.001 TYR A 297 PHE 0.004 0.001 PHE B 102 TRP 0.015 0.002 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6592) covalent geometry : angle 0.50871 ( 9160) hydrogen bonds : bond 0.03383 ( 264) hydrogen bonds : angle 3.53618 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.232 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: A 24 ARG cc_start: 0.6377 (tmt170) cc_final: 0.5558 (tpt-90) REVERT: A 103 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8088 (tt0) REVERT: A 124 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: A 142 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8048 (mtm180) REVERT: A 196 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8645 (mm-30) REVERT: A 332 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7741 (tm-30) REVERT: B 17 GLU cc_start: 0.8071 (tt0) cc_final: 0.7785 (mt-10) REVERT: B 24 ARG cc_start: 0.5931 (tmt170) cc_final: 0.2035 (mtm180) REVERT: B 85 ASP cc_start: 0.7813 (t0) cc_final: 0.7560 (t0) REVERT: B 142 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7889 (mtm180) REVERT: B 169 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7126 (tm-30) REVERT: B 225 ARG cc_start: 0.8577 (mtt90) cc_final: 0.8277 (mtt90) REVERT: B 312 GLU cc_start: 0.8794 (tt0) cc_final: 0.8445 (tt0) outliers start: 33 outliers final: 25 residues processed: 92 average time/residue: 0.1022 time to fit residues: 12.1755 Evaluate side-chains 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 0.0970 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.167590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122948 restraints weight = 6565.004| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.96 r_work: 0.3246 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6592 Z= 0.121 Angle : 0.488 5.832 9160 Z= 0.260 Chirality : 0.039 0.170 1008 Planarity : 0.003 0.030 1028 Dihedral : 22.813 104.077 1304 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.36 % Allowed : 23.21 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.36), residues: 666 helix: 2.08 (0.33), residues: 267 sheet: -0.86 (0.78), residues: 46 loop : -0.40 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.017 0.001 TYR A 297 PHE 0.005 0.001 PHE B 87 TRP 0.013 0.001 TRP B 156 HIS 0.001 0.000 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6592) covalent geometry : angle 0.48847 ( 9160) hydrogen bonds : bond 0.02955 ( 264) hydrogen bonds : angle 3.42342 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.184 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: A 24 ARG cc_start: 0.6254 (tmt170) cc_final: 0.5424 (tpt-90) REVERT: A 29 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7665 (mmm-85) REVERT: A 103 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8052 (tt0) REVERT: A 124 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: A 142 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8000 (mtm180) REVERT: A 196 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8627 (mm-30) REVERT: A 332 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 17 GLU cc_start: 0.8052 (tt0) cc_final: 0.7746 (mt-10) REVERT: B 24 ARG cc_start: 0.5900 (tmt170) cc_final: 0.2035 (mtm180) REVERT: B 85 ASP cc_start: 0.7733 (t0) cc_final: 0.7443 (t0) REVERT: B 142 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7865 (mtm180) REVERT: B 169 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7099 (tm-30) REVERT: B 202 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7197 (tp30) REVERT: B 225 ARG cc_start: 0.8535 (mtt90) cc_final: 0.8264 (mtt90) REVERT: B 312 GLU cc_start: 0.8814 (tt0) cc_final: 0.8465 (tt0) outliers start: 30 outliers final: 22 residues processed: 91 average time/residue: 0.0965 time to fit residues: 11.3487 Evaluate side-chains 95 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 0.1980 chunk 26 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.166704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120978 restraints weight = 6622.676| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.01 r_work: 0.3229 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6592 Z= 0.130 Angle : 0.492 5.746 9160 Z= 0.260 Chirality : 0.039 0.169 1008 Planarity : 0.003 0.030 1028 Dihedral : 22.836 106.472 1304 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.82 % Allowed : 23.75 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.36), residues: 666 helix: 2.10 (0.33), residues: 267 sheet: -0.79 (0.78), residues: 46 loop : -0.39 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.017 0.001 TYR A 297 PHE 0.004 0.001 PHE B 87 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6592) covalent geometry : angle 0.49156 ( 9160) hydrogen bonds : bond 0.03036 ( 264) hydrogen bonds : angle 3.42257 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1901.52 seconds wall clock time: 33 minutes 10.97 seconds (1990.97 seconds total)