Starting phenix.real_space_refine on Wed Feb 4 04:37:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khg_62339/02_2026/9khg_62339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khg_62339/02_2026/9khg_62339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9khg_62339/02_2026/9khg_62339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khg_62339/02_2026/9khg_62339.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9khg_62339/02_2026/9khg_62339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khg_62339/02_2026/9khg_62339.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 40 5.16 5 C 5828 2.51 5 N 1384 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "C" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "D" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.06, per 1000 atoms: 0.24 Number of scatterers: 8670 At special positions: 0 Unit cell: (112.36, 113.42, 79.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 40 16.00 O 1416 8.00 N 1384 7.00 C 5828 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: 0.87 Conformation dependent library (CDL) restraints added in 306.9 milliseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 3 sheets defined 73.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 62 through 90 Proline residue: A 84 - end of helix removed outlier: 3.630A pdb=" N PHE A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 97 through 116 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 164 through 170 removed outlier: 4.013A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 177 through 191 removed outlier: 4.207A pdb=" N VAL A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 removed outlier: 3.617A pdb=" N ALA A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 281 through 313 removed outlier: 3.724A pdb=" N VAL A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 Proline residue: B 84 - end of helix removed outlier: 3.621A pdb=" N PHE B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 116 Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.509A pdb=" N ILE B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.910A pdb=" N ARG B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.502A pdb=" N ARG B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 removed outlier: 4.220A pdb=" N VAL B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 225 removed outlier: 3.608A pdb=" N ALA B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 Processing helix chain 'B' and resid 281 through 313 removed outlier: 3.722A pdb=" N VAL B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 90 Proline residue: C 84 - end of helix removed outlier: 3.644A pdb=" N PHE C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 118 removed outlier: 4.124A pdb=" N PHE C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 144 through 152 Processing helix chain 'C' and resid 155 through 161 Processing helix chain 'C' and resid 164 through 170 removed outlier: 4.100A pdb=" N ARG C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 177 through 191 removed outlier: 4.199A pdb=" N VAL C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 225 removed outlier: 3.616A pdb=" N ALA C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 224 " --> pdb=" O TYR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 Processing helix chain 'C' and resid 281 through 313 removed outlier: 3.745A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 Proline residue: D 84 - end of helix removed outlier: 3.576A pdb=" N PHE D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 155 through 161 Processing helix chain 'D' and resid 164 through 170 removed outlier: 4.125A pdb=" N ARG D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 4.054A pdb=" N PHE D 176 " --> pdb=" O ILE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 191 removed outlier: 4.240A pdb=" N VAL D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 225 removed outlier: 3.614A pdb=" N ALA D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 224 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 313 removed outlier: 3.704A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.828A pdb=" N TYR A 120 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 129 " --> pdb=" O TYR A 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.822A pdb=" N TYR C 120 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 129 " --> pdb=" O TYR C 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.853A pdb=" N TYR D 120 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 129 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D 122 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG D 127 " --> pdb=" O ASP D 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 538 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1256 1.31 - 1.44: 2836 1.44 - 1.56: 4779 1.56 - 1.68: 1 1.68 - 1.81: 68 Bond restraints: 8940 Sorted by residual: bond pdb=" C TYR D 139 " pdb=" N LEU D 140 " ideal model delta sigma weight residual 1.334 1.210 0.124 1.27e-02 6.20e+03 9.59e+01 bond pdb=" C ARG D 96 " pdb=" N LEU D 97 " ideal model delta sigma weight residual 1.332 1.417 -0.086 1.52e-02 4.33e+03 3.18e+01 bond pdb=" C ARG D 168 " pdb=" O ARG D 168 " ideal model delta sigma weight residual 1.236 1.189 0.046 1.28e-02 6.10e+03 1.31e+01 bond pdb=" CA ALA B 270 " pdb=" CB ALA B 270 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.74e-02 3.30e+03 1.23e+01 bond pdb=" CA ALA C 270 " pdb=" CB ALA C 270 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.74e-02 3.30e+03 1.23e+01 ... (remaining 8935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11624 1.81 - 3.61: 359 3.61 - 5.42: 113 5.42 - 7.23: 22 7.23 - 9.04: 18 Bond angle restraints: 12136 Sorted by residual: angle pdb=" N VAL A 272 " pdb=" CA VAL A 272 " pdb=" C VAL A 272 " ideal model delta sigma weight residual 110.74 102.19 8.55 9.10e-01 1.21e+00 8.82e+01 angle pdb=" N VAL D 272 " pdb=" CA VAL D 272 " pdb=" C VAL D 272 " ideal model delta sigma weight residual 110.74 102.26 8.48 9.10e-01 1.21e+00 8.69e+01 angle pdb=" N VAL C 272 " pdb=" CA VAL C 272 " pdb=" C VAL C 272 " ideal model delta sigma weight residual 110.74 102.34 8.40 9.10e-01 1.21e+00 8.52e+01 angle pdb=" N VAL B 272 " pdb=" CA VAL B 272 " pdb=" C VAL B 272 " ideal model delta sigma weight residual 110.74 102.36 8.38 9.10e-01 1.21e+00 8.48e+01 angle pdb=" N TRP B 64 " pdb=" CA TRP B 64 " pdb=" C TRP B 64 " ideal model delta sigma weight residual 111.28 119.70 -8.42 1.09e+00 8.42e-01 5.96e+01 ... (remaining 12131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4284 17.99 - 35.98: 628 35.98 - 53.97: 158 53.97 - 71.97: 25 71.97 - 89.96: 5 Dihedral angle restraints: 5100 sinusoidal: 2056 harmonic: 3044 Sorted by residual: dihedral pdb=" CA SER B 142 " pdb=" C SER B 142 " pdb=" N HIS B 143 " pdb=" CA HIS B 143 " ideal model delta harmonic sigma weight residual 180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE A 176 " pdb=" C PHE A 176 " pdb=" N ARG A 177 " pdb=" CA ARG A 177 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE D 176 " pdb=" C PHE D 176 " pdb=" N ARG D 177 " pdb=" CA ARG D 177 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1163 0.063 - 0.126: 125 0.126 - 0.190: 21 0.190 - 0.253: 12 0.253 - 0.316: 3 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA THR A 271 " pdb=" N THR A 271 " pdb=" C THR A 271 " pdb=" CB THR A 271 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA THR C 271 " pdb=" N THR C 271 " pdb=" C THR C 271 " pdb=" CB THR C 271 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1321 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 268 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C THR A 268 " -0.061 2.00e-02 2.50e+03 pdb=" O THR A 268 " 0.022 2.00e-02 2.50e+03 pdb=" N MET A 269 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 272 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C VAL D 272 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL D 272 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY D 273 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 272 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C VAL B 272 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL B 272 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY B 273 " -0.021 2.00e-02 2.50e+03 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 2479 2.80 - 3.39: 9994 3.39 - 3.97: 15860 3.97 - 4.56: 22574 4.56 - 5.14: 32716 Nonbonded interactions: 83623 Sorted by model distance: nonbonded pdb=" O ALA A 270 " pdb=" OG1 THR A 271 " model vdw 2.217 3.040 nonbonded pdb=" O ILE C 157 " pdb=" OG SER C 161 " model vdw 2.221 3.040 nonbonded pdb=" O ARG D 168 " pdb=" N LEU D 171 " model vdw 2.223 3.120 nonbonded pdb=" O ILE B 157 " pdb=" OG SER B 161 " model vdw 2.225 3.040 nonbonded pdb=" O ILE D 157 " pdb=" OG SER D 161 " model vdw 2.238 3.040 ... (remaining 83618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 58 through 313) selection = chain 'B' selection = 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: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.450 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.005 0.124 8940 Z= 0.305 Angle : 0.856 9.037 12136 Z= 0.558 Chirality : 0.049 0.316 1324 Planarity : 0.006 0.039 1464 Dihedral : 17.395 89.958 3156 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.05 % Favored : 96.56 % Rotamer: Outliers : 1.32 % Allowed : 26.86 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1016 helix: 0.91 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -0.28 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 174 TYR 0.013 0.002 TYR A 120 PHE 0.018 0.002 PHE A 98 TRP 0.009 0.001 TRP B 255 HIS 0.004 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 8940) covalent geometry : angle 0.85640 (12136) hydrogen bonds : bond 0.13225 ( 538) hydrogen bonds : angle 5.50097 ( 1584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 PHE cc_start: 0.8485 (t80) cc_final: 0.8275 (t80) REVERT: A 96 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7429 (mtm-85) REVERT: A 146 MET cc_start: 0.7855 (ttm) cc_final: 0.7527 (ttm) REVERT: A 269 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7879 (ttt) REVERT: A 276 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7684 (p0) REVERT: B 131 LYS cc_start: 0.8383 (tppt) cc_final: 0.7814 (mmmt) REVERT: C 96 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7515 (mtm-85) REVERT: C 121 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7548 (tpp80) REVERT: C 151 CYS cc_start: 0.8268 (t) cc_final: 0.7772 (m) REVERT: C 244 TYR cc_start: 0.7976 (t80) cc_final: 0.7544 (t80) REVERT: C 269 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7796 (ttt) REVERT: D 153 PRO cc_start: 0.7779 (Cg_exo) cc_final: 0.7479 (Cg_endo) REVERT: D 164 HIS cc_start: 0.7888 (m-70) cc_final: 0.7495 (m-70) REVERT: D 276 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7793 (p0) outliers start: 12 outliers final: 2 residues processed: 209 average time/residue: 0.0804 time to fit residues: 23.6938 Evaluate side-chains 187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 309 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.202440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132986 restraints weight = 9716.942| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.01 r_work: 0.3311 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8940 Z= 0.141 Angle : 0.549 9.739 12136 Z= 0.295 Chirality : 0.039 0.221 1324 Planarity : 0.004 0.032 1464 Dihedral : 6.112 57.245 1183 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.29 % Allowed : 22.26 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.26), residues: 1016 helix: 1.46 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -0.70 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 174 TYR 0.012 0.001 TYR D 220 PHE 0.019 0.002 PHE A 98 TRP 0.011 0.001 TRP B 255 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8940) covalent geometry : angle 0.54941 (12136) hydrogen bonds : bond 0.04999 ( 538) hydrogen bonds : angle 4.08110 ( 1584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7358 (mtm180) REVERT: B 175 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8048 (mp) REVERT: B 251 GLU cc_start: 0.8466 (mp0) cc_final: 0.8135 (mp0) REVERT: C 86 GLU cc_start: 0.7750 (tp30) cc_final: 0.7380 (tt0) REVERT: C 96 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7430 (mtm180) REVERT: C 244 TYR cc_start: 0.8091 (t80) cc_final: 0.7525 (t80) REVERT: D 72 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7265 (tp) REVERT: D 164 HIS cc_start: 0.8164 (m-70) cc_final: 0.7900 (m-70) REVERT: D 251 GLU cc_start: 0.8454 (mp0) cc_final: 0.8123 (mp0) outliers start: 30 outliers final: 14 residues processed: 207 average time/residue: 0.0808 time to fit residues: 23.8140 Evaluate side-chains 187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 113 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 67 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 92 optimal weight: 0.0000 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.206317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132118 restraints weight = 9547.560| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.34 r_work: 0.3399 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8940 Z= 0.136 Angle : 0.530 9.463 12136 Z= 0.275 Chirality : 0.040 0.264 1324 Planarity : 0.003 0.032 1464 Dihedral : 5.167 47.420 1177 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.95 % Allowed : 22.04 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.26), residues: 1016 helix: 1.75 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.49 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 174 TYR 0.013 0.001 TYR B 220 PHE 0.019 0.001 PHE B 144 TRP 0.009 0.001 TRP D 255 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8940) covalent geometry : angle 0.52988 (12136) hydrogen bonds : bond 0.04639 ( 538) hydrogen bonds : angle 3.84881 ( 1584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.8067 (mtm180) cc_final: 0.7364 (mtm180) REVERT: A 157 ILE cc_start: 0.8577 (mt) cc_final: 0.8350 (mt) REVERT: A 251 GLU cc_start: 0.8592 (mp0) cc_final: 0.8326 (mp0) REVERT: A 295 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6491 (t70) REVERT: B 175 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8214 (mp) REVERT: C 86 GLU cc_start: 0.7952 (tp30) cc_final: 0.7651 (tt0) REVERT: C 96 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7459 (mtm180) REVERT: C 121 ARG cc_start: 0.7580 (tpp80) cc_final: 0.6819 (tpp80) REVERT: C 233 TYR cc_start: 0.8605 (t80) cc_final: 0.8390 (t80) REVERT: D 71 PHE cc_start: 0.8244 (t80) cc_final: 0.7952 (t80) REVERT: D 72 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7406 (tp) REVERT: D 109 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7852 (mm) REVERT: D 146 MET cc_start: 0.8553 (tpp) cc_final: 0.8330 (tpp) REVERT: D 156 LEU cc_start: 0.8503 (mm) cc_final: 0.8290 (mm) REVERT: D 164 HIS cc_start: 0.8123 (m-70) cc_final: 0.7799 (m-70) REVERT: D 178 VAL cc_start: 0.8229 (m) cc_final: 0.7997 (t) outliers start: 36 outliers final: 14 residues processed: 204 average time/residue: 0.0663 time to fit residues: 19.8861 Evaluate side-chains 187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.0270 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS C 305 ASN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.205601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131212 restraints weight = 9757.000| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.59 r_work: 0.3368 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8940 Z= 0.132 Angle : 0.528 9.143 12136 Z= 0.272 Chirality : 0.043 0.393 1324 Planarity : 0.003 0.025 1464 Dihedral : 4.328 23.595 1168 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.28 % Allowed : 21.16 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.26), residues: 1016 helix: 1.87 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.43 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 174 TYR 0.013 0.001 TYR A 220 PHE 0.022 0.002 PHE B 98 TRP 0.009 0.001 TRP D 255 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8940) covalent geometry : angle 0.52805 (12136) hydrogen bonds : bond 0.04400 ( 538) hydrogen bonds : angle 3.73252 ( 1584) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.270 Fit side-chains REVERT: A 96 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7417 (mtm180) REVERT: A 251 GLU cc_start: 0.8660 (mp0) cc_final: 0.8418 (mp0) REVERT: A 295 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6584 (t70) REVERT: B 234 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8801 (p) REVERT: B 251 GLU cc_start: 0.8642 (mp0) cc_final: 0.8358 (mp0) REVERT: C 86 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: C 96 ARG cc_start: 0.8112 (mtm180) cc_final: 0.7416 (mtm180) REVERT: C 121 ARG cc_start: 0.7635 (tpp80) cc_final: 0.6785 (tpp80) REVERT: C 234 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8800 (p) REVERT: C 251 GLU cc_start: 0.8656 (mp0) cc_final: 0.8399 (mp0) REVERT: C 295 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6603 (t70) REVERT: D 71 PHE cc_start: 0.8256 (t80) cc_final: 0.7958 (t80) REVERT: D 109 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7863 (mm) REVERT: D 156 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8272 (mm) REVERT: D 164 HIS cc_start: 0.8078 (m-70) cc_final: 0.7713 (m-70) REVERT: D 178 VAL cc_start: 0.8243 (m) cc_final: 0.8009 (t) REVERT: D 234 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8737 (p) REVERT: D 251 GLU cc_start: 0.8650 (mp0) cc_final: 0.8286 (mp0) REVERT: D 295 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6476 (t70) outliers start: 39 outliers final: 16 residues processed: 196 average time/residue: 0.0560 time to fit residues: 16.4760 Evaluate side-chains 191 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 0.0570 chunk 99 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.203769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129704 restraints weight = 9536.353| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.37 r_work: 0.3375 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8940 Z= 0.117 Angle : 0.518 10.612 12136 Z= 0.264 Chirality : 0.038 0.240 1324 Planarity : 0.003 0.026 1464 Dihedral : 4.249 21.954 1168 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.63 % Allowed : 23.03 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.26), residues: 1016 helix: 1.97 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.32 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 174 TYR 0.012 0.001 TYR A 220 PHE 0.021 0.002 PHE D 184 TRP 0.008 0.001 TRP D 255 HIS 0.005 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8940) covalent geometry : angle 0.51822 (12136) hydrogen bonds : bond 0.04178 ( 538) hydrogen bonds : angle 3.66064 ( 1584) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7283 (mtm180) REVERT: A 234 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8784 (p) REVERT: A 251 GLU cc_start: 0.8618 (mp0) cc_final: 0.8408 (mp0) REVERT: A 295 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6486 (t70) REVERT: B 109 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7950 (mm) REVERT: B 234 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8744 (p) REVERT: C 86 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: C 121 ARG cc_start: 0.7698 (tpp80) cc_final: 0.6772 (tpp80) REVERT: C 251 GLU cc_start: 0.8616 (mp0) cc_final: 0.8395 (mp0) REVERT: D 71 PHE cc_start: 0.8150 (t80) cc_final: 0.7859 (t80) REVERT: D 109 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7925 (mm) REVERT: D 164 HIS cc_start: 0.7947 (m-70) cc_final: 0.7401 (m-70) REVERT: D 234 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8704 (p) outliers start: 24 outliers final: 10 residues processed: 182 average time/residue: 0.0599 time to fit residues: 16.3635 Evaluate side-chains 178 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS C 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.205999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131820 restraints weight = 9591.368| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.65 r_work: 0.3368 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8940 Z= 0.125 Angle : 0.503 7.205 12136 Z= 0.262 Chirality : 0.038 0.235 1324 Planarity : 0.003 0.028 1464 Dihedral : 4.211 22.067 1168 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.40 % Allowed : 23.25 % Favored : 73.36 % 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 are not related in a simple way. whole: 1.99 (0.26), residues: 1016 helix: 1.98 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.21 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 283 TYR 0.016 0.001 TYR D 233 PHE 0.022 0.002 PHE D 184 TRP 0.008 0.001 TRP D 255 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8940) covalent geometry : angle 0.50288 (12136) hydrogen bonds : bond 0.04139 ( 538) hydrogen bonds : angle 3.57638 ( 1584) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.318 Fit side-chains REVERT: A 96 ARG cc_start: 0.7895 (mtm180) cc_final: 0.7265 (mtm180) REVERT: A 234 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 295 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6475 (t70) REVERT: B 109 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7977 (mm) REVERT: B 156 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8333 (mm) REVERT: B 234 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8720 (p) REVERT: B 251 GLU cc_start: 0.8588 (mp0) cc_final: 0.8248 (mp0) REVERT: C 86 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: C 121 ARG cc_start: 0.7705 (tpp80) cc_final: 0.6792 (tpp80) REVERT: C 234 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8729 (p) REVERT: C 295 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6490 (t70) REVERT: D 71 PHE cc_start: 0.8184 (t80) cc_final: 0.7886 (t80) REVERT: D 96 ARG cc_start: 0.8310 (mtt180) cc_final: 0.7926 (mmm-85) REVERT: D 109 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7887 (mm) REVERT: D 164 HIS cc_start: 0.7981 (m-70) cc_final: 0.7451 (m-70) REVERT: D 234 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8567 (p) REVERT: D 251 GLU cc_start: 0.8670 (mp0) cc_final: 0.8333 (mp0) REVERT: D 295 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6342 (t70) outliers start: 31 outliers final: 12 residues processed: 181 average time/residue: 0.0707 time to fit residues: 18.9264 Evaluate side-chains 181 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.206073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131103 restraints weight = 9761.009| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.66 r_work: 0.3357 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8940 Z= 0.129 Angle : 0.506 7.112 12136 Z= 0.264 Chirality : 0.038 0.231 1324 Planarity : 0.003 0.029 1464 Dihedral : 4.187 21.604 1168 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.29 % Allowed : 24.01 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.26), residues: 1016 helix: 2.01 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.14 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 168 TYR 0.013 0.001 TYR A 220 PHE 0.023 0.001 PHE D 184 TRP 0.009 0.001 TRP B 172 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8940) covalent geometry : angle 0.50612 (12136) hydrogen bonds : bond 0.04115 ( 538) hydrogen bonds : angle 3.53727 ( 1584) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.215 Fit side-chains REVERT: A 96 ARG cc_start: 0.7891 (mtm180) cc_final: 0.7261 (mtm180) REVERT: A 234 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8759 (p) REVERT: A 295 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6538 (t70) REVERT: B 109 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7998 (mm) REVERT: B 156 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8376 (mm) REVERT: B 234 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8738 (p) REVERT: C 121 ARG cc_start: 0.7776 (tpp80) cc_final: 0.6869 (tpp80) REVERT: C 234 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8756 (p) REVERT: C 251 GLU cc_start: 0.8725 (mp0) cc_final: 0.8496 (mp0) REVERT: C 295 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6560 (t70) REVERT: D 71 PHE cc_start: 0.8287 (t80) cc_final: 0.7987 (t80) REVERT: D 96 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7943 (mmm-85) REVERT: D 109 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7939 (mm) REVERT: D 164 HIS cc_start: 0.7999 (m-70) cc_final: 0.7430 (m-70) REVERT: D 234 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8709 (p) REVERT: D 295 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6443 (t70) outliers start: 30 outliers final: 14 residues processed: 179 average time/residue: 0.0639 time to fit residues: 16.7454 Evaluate side-chains 184 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 0.0270 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.200487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124977 restraints weight = 9559.676| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.45 r_work: 0.3309 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8940 Z= 0.136 Angle : 0.521 7.122 12136 Z= 0.273 Chirality : 0.039 0.228 1324 Planarity : 0.003 0.029 1464 Dihedral : 4.201 21.370 1168 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.18 % Allowed : 24.23 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.26), residues: 1016 helix: 1.99 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.14 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 168 TYR 0.013 0.001 TYR B 220 PHE 0.025 0.002 PHE D 98 TRP 0.008 0.001 TRP D 255 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8940) covalent geometry : angle 0.52057 (12136) hydrogen bonds : bond 0.04117 ( 538) hydrogen bonds : angle 3.51633 ( 1584) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.226 Fit side-chains REVERT: A 96 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7250 (mtm180) REVERT: A 116 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7904 (t80) REVERT: A 234 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8728 (p) REVERT: A 295 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6412 (t70) REVERT: B 109 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7909 (mm) REVERT: B 156 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8306 (mm) REVERT: B 234 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8737 (p) REVERT: B 251 GLU cc_start: 0.8762 (mp0) cc_final: 0.8460 (mp0) REVERT: C 121 ARG cc_start: 0.7728 (tpp80) cc_final: 0.6818 (tpp80) REVERT: C 234 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8734 (p) REVERT: C 251 GLU cc_start: 0.8715 (mp0) cc_final: 0.8398 (mp0) REVERT: C 295 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6374 (t70) REVERT: D 96 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7904 (mmm-85) REVERT: D 109 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7913 (mm) REVERT: D 234 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8727 (p) REVERT: D 295 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6376 (t70) outliers start: 29 outliers final: 15 residues processed: 177 average time/residue: 0.0734 time to fit residues: 19.0554 Evaluate side-chains 186 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.199212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123518 restraints weight = 9501.741| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.43 r_work: 0.3275 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8940 Z= 0.157 Angle : 0.547 7.170 12136 Z= 0.286 Chirality : 0.039 0.228 1324 Planarity : 0.003 0.028 1464 Dihedral : 4.220 21.511 1168 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.96 % Allowed : 25.11 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.26), residues: 1016 helix: 1.97 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.11 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.015 0.001 TYR B 220 PHE 0.025 0.002 PHE D 184 TRP 0.009 0.001 TRP D 255 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8940) covalent geometry : angle 0.54674 (12136) hydrogen bonds : bond 0.04226 ( 538) hydrogen bonds : angle 3.52205 ( 1584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.250 Fit side-chains REVERT: A 96 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7255 (mtm180) REVERT: A 234 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8719 (p) REVERT: A 295 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6431 (t70) REVERT: B 109 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7944 (mm) REVERT: B 156 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8263 (mm) REVERT: B 234 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8722 (p) REVERT: B 251 GLU cc_start: 0.8742 (mp0) cc_final: 0.8453 (mp0) REVERT: C 96 ARG cc_start: 0.8390 (mtm180) cc_final: 0.7664 (mtm180) REVERT: C 121 ARG cc_start: 0.7755 (tpp80) cc_final: 0.6853 (tpp80) REVERT: C 234 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8716 (p) REVERT: C 251 GLU cc_start: 0.8761 (mp0) cc_final: 0.8448 (mp0) REVERT: C 295 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6386 (t70) REVERT: D 71 PHE cc_start: 0.8252 (t80) cc_final: 0.7961 (t80) REVERT: D 96 ARG cc_start: 0.8296 (mtt180) cc_final: 0.7935 (mmm-85) REVERT: D 109 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7920 (mm) REVERT: D 234 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8684 (p) REVERT: D 295 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6438 (t70) outliers start: 27 outliers final: 15 residues processed: 173 average time/residue: 0.0662 time to fit residues: 16.6645 Evaluate side-chains 185 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.198567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124544 restraints weight = 9580.223| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.95 r_work: 0.3212 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8940 Z= 0.135 Angle : 0.537 7.118 12136 Z= 0.280 Chirality : 0.038 0.227 1324 Planarity : 0.003 0.028 1464 Dihedral : 4.171 21.451 1168 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.85 % Allowed : 25.33 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.27), residues: 1016 helix: 2.02 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.08 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.014 0.001 TYR A 220 PHE 0.028 0.002 PHE D 184 TRP 0.008 0.001 TRP D 255 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8940) covalent geometry : angle 0.53747 (12136) hydrogen bonds : bond 0.04106 ( 538) hydrogen bonds : angle 3.47929 ( 1584) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.267 Fit side-chains REVERT: A 96 ARG cc_start: 0.7933 (mtm180) cc_final: 0.7243 (mtm180) REVERT: A 234 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8618 (p) REVERT: A 295 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6290 (t70) REVERT: B 109 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7909 (mm) REVERT: B 116 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8049 (t80) REVERT: B 156 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8251 (mm) REVERT: B 234 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8635 (p) REVERT: B 251 GLU cc_start: 0.8661 (mp0) cc_final: 0.8349 (mp0) REVERT: C 96 ARG cc_start: 0.8383 (mtm180) cc_final: 0.7643 (mtm180) REVERT: C 234 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8634 (p) REVERT: C 251 GLU cc_start: 0.8704 (mp0) cc_final: 0.8398 (mp0) REVERT: C 295 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6210 (t70) REVERT: D 71 PHE cc_start: 0.8142 (t80) cc_final: 0.7842 (t80) REVERT: D 96 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7954 (mmm-85) REVERT: D 109 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7894 (mm) REVERT: D 234 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8597 (p) REVERT: D 295 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6277 (t70) outliers start: 26 outliers final: 14 residues processed: 172 average time/residue: 0.0645 time to fit residues: 16.1929 Evaluate side-chains 180 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 52 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 63 optimal weight: 0.0170 chunk 57 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.201278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125504 restraints weight = 9489.557| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.43 r_work: 0.3306 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8940 Z= 0.125 Angle : 0.534 7.113 12136 Z= 0.277 Chirality : 0.038 0.224 1324 Planarity : 0.003 0.028 1464 Dihedral : 4.127 21.568 1168 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.63 % Allowed : 25.99 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.27), residues: 1016 helix: 2.09 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.05 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.013 0.001 TYR A 220 PHE 0.029 0.001 PHE D 184 TRP 0.007 0.001 TRP D 255 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8940) covalent geometry : angle 0.53388 (12136) hydrogen bonds : bond 0.04004 ( 538) hydrogen bonds : angle 3.44648 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.54 seconds wall clock time: 40 minutes 17.01 seconds (2417.01 seconds total)