Starting phenix.real_space_refine on Thu Sep 10 23:55:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w34_65590/09_2026/9w34_65590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w34_65590/09_2026/9w34_65590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w34_65590/09_2026/9w34_65590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w34_65590/09_2026/9w34_65590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w34_65590/09_2026/9w34_65590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w34_65590/09_2026/9w34_65590.map" } resolution = 3.21 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= 0.004 sd= 0.050 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 3541 2.51 5 N 946 2.21 5 O 1027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5555 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1848 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 217} Chain: "C" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1901 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1806 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Time building chain proxies: 1.40, per 1000 atoms: 0.25 Number of scatterers: 5555 At special positions: 0 Unit cell: (96.005, 100.225, 83.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1027 8.00 N 946 7.00 C 3541 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: 0.37 Conformation dependent library (CDL) restraints added in 240.4 milliseconds 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1322 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 11 sheets defined 14.1% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.686A pdb=" N ASN B 87 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.984A pdb=" N ARG B 151 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'C' and resid 43 through 48 removed outlier: 3.592A pdb=" N ILE C 47 " --> pdb=" O MET C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.565A pdb=" N GLU C 65 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 143 through 149 removed outlier: 3.850A pdb=" N LEU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.675A pdb=" N ALA C 245 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 109 removed outlier: 3.937A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.685A pdb=" N GLN A 164 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 165 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.532A pdb=" N THR A 216 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.502A pdb=" N ILE B 23 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.695A pdb=" N VAL B 226 " --> pdb=" O TRP B 71 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.717A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 212 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 39 through 40 removed outlier: 4.380A pdb=" N ALA A 248 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 76 removed outlier: 6.969A pdb=" N VAL A 239 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A 71 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 237 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 73 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL A 235 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLU A 75 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE A 233 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 53 removed outlier: 4.620A pdb=" N GLY C 214 " --> pdb=" O MET C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 51 through 53 removed outlier: 4.620A pdb=" N GLY C 214 " --> pdb=" O MET C 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.854A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR C 193 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR C 134 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N PHE C 195 " --> pdb=" O CYS C 132 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS C 132 " --> pdb=" O PHE C 195 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN C 197 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE C 130 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN C 199 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C 128 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 133 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 151 " --> pdb=" O TYR C 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.396A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 90 through 94 removed outlier: 4.062A pdb=" N ALA A 169 " --> pdb=" O PHE A 147 " (cutoff:3.500A) 161 hydrogen bonds defined for protein. 390 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: 0.86 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1800 1.35 - 1.46: 1374 1.46 - 1.58: 2463 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 5705 Sorted by residual: bond pdb=" CA ILE B 127 " pdb=" C ILE B 127 " ideal model delta sigma weight residual 1.528 1.520 0.008 7.70e-03 1.69e+04 1.13e+00 bond pdb=" CB MET C 124 " pdb=" CG MET C 124 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.62e-01 bond pdb=" CA PRO C 135 " pdb=" C PRO C 135 " ideal model delta sigma weight residual 1.514 1.519 -0.005 5.50e-03 3.31e+04 6.75e-01 bond pdb=" C GLU B 57 " pdb=" N THR B 58 " ideal model delta sigma weight residual 1.324 1.344 -0.020 2.56e-02 1.53e+03 6.17e-01 bond pdb=" CB MET A 136 " pdb=" CG MET A 136 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.11e-01 ... (remaining 5700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 7653 1.69 - 3.37: 111 3.37 - 5.05: 5 5.05 - 6.74: 3 6.74 - 8.42: 2 Bond angle restraints: 7774 Sorted by residual: angle pdb=" CB MET C 124 " pdb=" CG MET C 124 " pdb=" SD MET C 124 " ideal model delta sigma weight residual 112.70 121.12 -8.42 3.00e+00 1.11e-01 7.89e+00 angle pdb=" N GLY B 218 " pdb=" CA GLY B 218 " pdb=" C GLY B 218 " ideal model delta sigma weight residual 110.91 115.00 -4.09 1.49e+00 4.50e-01 7.53e+00 angle pdb=" N GLY A 218 " pdb=" CA GLY A 218 " pdb=" C GLY A 218 " ideal model delta sigma weight residual 110.29 113.47 -3.18 1.28e+00 6.10e-01 6.16e+00 angle pdb=" CB MET A 136 " pdb=" CG MET A 136 " pdb=" SD MET A 136 " ideal model delta sigma weight residual 112.70 119.55 -6.85 3.00e+00 1.11e-01 5.21e+00 angle pdb=" CG1 ILE C 88 " pdb=" CB ILE C 88 " pdb=" CG2 ILE C 88 " ideal model delta sigma weight residual 110.70 105.33 5.37 3.00e+00 1.11e-01 3.20e+00 ... (remaining 7769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2941 17.98 - 35.96: 335 35.96 - 53.94: 77 53.94 - 71.92: 12 71.92 - 89.90: 4 Dihedral angle restraints: 3369 sinusoidal: 1318 harmonic: 2051 Sorted by residual: dihedral pdb=" CA ASN B 179 " pdb=" C ASN B 179 " pdb=" N LEU B 180 " pdb=" CA LEU B 180 " ideal model delta harmonic sigma weight residual -180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB GLU A 227 " pdb=" CG GLU A 227 " pdb=" CD GLU A 227 " pdb=" OE1 GLU A 227 " ideal model delta sinusoidal sigma weight residual 0.00 -89.90 89.90 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP C 87 " pdb=" CB ASP C 87 " pdb=" CG ASP C 87 " pdb=" OD1 ASP C 87 " ideal model delta sinusoidal sigma weight residual -30.00 -86.17 56.17 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 3366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 535 0.030 - 0.060: 220 0.060 - 0.090: 60 0.090 - 0.119: 38 0.119 - 0.149: 11 Chirality restraints: 864 Sorted by residual: chirality pdb=" CB ILE C 88 " pdb=" CA ILE C 88 " pdb=" CG1 ILE C 88 " pdb=" CG2 ILE C 88 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE B 127 " pdb=" N ILE B 127 " pdb=" C ILE B 127 " pdb=" CB ILE B 127 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE C 167 " pdb=" N ILE C 167 " pdb=" C ILE C 167 " pdb=" CB ILE C 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 861 not shown) Planarity restraints: 1003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 226 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO B 227 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 26 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C GLN B 26 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN B 26 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU B 27 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 200 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.65e+00 pdb=" N PRO B 201 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " 0.018 5.00e-02 4.00e+02 ... (remaining 1000 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 3499 3.07 - 3.52: 5367 3.52 - 3.98: 8637 3.98 - 4.44: 10444 4.44 - 4.90: 16584 Nonbonded interactions: 44531 Sorted by model distance: nonbonded pdb=" N THR A 57 " pdb=" OG1 THR A 57 " model vdw 2.606 2.496 nonbonded pdb=" N VAL A 54 " pdb=" N SER A 55 " model vdw 2.622 2.560 nonbonded pdb=" C SER B 73 " pdb=" OG SER B 73 " model vdw 2.631 2.616 nonbonded pdb=" CG LYS B 116 " pdb=" NZ LYS B 116 " model vdw 2.632 2.816 nonbonded pdb=" N ASN C 199 " pdb=" O ASN C 199 " model vdw 2.632 2.496 ... (remaining 44526 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.230 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.002 0.026 5705 Z= 0.102 Angle : 0.508 8.425 7774 Z= 0.267 Chirality : 0.041 0.149 864 Planarity : 0.003 0.037 1003 Dihedral : 15.762 89.895 2047 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.61 % Allowed : 22.84 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.80 (0.31), residues: 701 helix: -2.20 (0.63), residues: 62 sheet: 0.24 (0.38), residues: 191 loop : -0.60 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.022 0.001 TYR A 209 PHE 0.016 0.001 PHE A 233 TRP 0.008 0.001 TRP C 169 HIS 0.002 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 5705) covalent geometry : angle 0.50773 / 0.27 ( 7774) hydrogen bonds : bond 0.22549 / 14.72 ( 142) hydrogen bonds : angle 9.56786 / 6.64 ( 390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.2470 (OUTLIER) cc_final: 0.1884 (tm-30) REVERT: B 119 GLN cc_start: 0.8147 (pm20) cc_final: 0.7077 (pt0) REVERT: B 129 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8329 (mm-30) REVERT: B 206 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7089 (mp-120) REVERT: C 18 ASP cc_start: 0.8540 (m-30) cc_final: 0.8268 (m-30) REVERT: C 43 MET cc_start: 0.8689 (mtp) cc_final: 0.8444 (mmm) REVERT: C 65 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8022 (mt-10) REVERT: C 157 PHE cc_start: 0.7362 (m-10) cc_final: 0.6987 (m-80) REVERT: C 178 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5267 (m-10) REVERT: C 229 ASP cc_start: 0.7389 (m-30) cc_final: 0.6949 (p0) REVERT: A 157 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: A 234 THR cc_start: 0.8350 (m) cc_final: 0.8071 (p) REVERT: A 290 MET cc_start: 0.6063 (mtm) cc_final: 0.5696 (mtp) outliers start: 16 outliers final: 9 residues processed: 103 average time/residue: 0.0611 time to fit residues: 8.6052 Evaluate side-chains 101 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 194 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN B 88 ASN B 176 GLN B 206 GLN B 240 ASN C 48 GLN C 101 ASN C 186 ASN A 87 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.164247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115113 restraints weight = 7303.203| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.24 r_work: 0.3195 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5705 Z= 0.168 Angle : 0.502 4.902 7774 Z= 0.260 Chirality : 0.042 0.141 864 Planarity : 0.004 0.043 1003 Dihedral : 6.818 55.216 788 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.55 % Allowed : 19.74 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.76 (0.31), residues: 701 helix: -2.23 (0.61), residues: 63 sheet: 0.54 (0.40), residues: 174 loop : -0.66 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.013 0.001 TYR B 100 PHE 0.018 0.001 PHE A 91 TRP 0.007 0.001 TRP A 249 HIS 0.002 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 5705) covalent geometry : angle 0.50179 / 0.26 ( 7774) hydrogen bonds : bond 0.03485 / 2.26 ( 142) hydrogen bonds : angle 6.09726 / 4.22 ( 390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.2557 (OUTLIER) cc_final: 0.1986 (tm-30) REVERT: B 119 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7080 (pt0) REVERT: B 176 GLN cc_start: 0.8608 (mm110) cc_final: 0.8352 (mm-40) REVERT: C 14 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7971 (tp) REVERT: C 18 ASP cc_start: 0.8574 (m-30) cc_final: 0.8333 (m-30) REVERT: C 54 GLU cc_start: 0.8865 (tt0) cc_final: 0.8525 (tt0) REVERT: C 65 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7956 (mt-10) REVERT: C 124 MET cc_start: 0.8423 (mmp) cc_final: 0.8175 (mmp) REVERT: C 229 ASP cc_start: 0.7572 (m-30) cc_final: 0.7099 (p0) REVERT: A 91 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.6724 (p90) REVERT: A 157 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 244 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8534 (ptmt) REVERT: A 290 MET cc_start: 0.6050 (mtm) cc_final: 0.5675 (mtp) outliers start: 34 outliers final: 24 residues processed: 106 average time/residue: 0.0640 time to fit residues: 9.2755 Evaluate side-chains 110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 288 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.165624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117075 restraints weight = 7127.417| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.07 r_work: 0.3219 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5705 Z= 0.149 Angle : 0.479 5.232 7774 Z= 0.248 Chirality : 0.041 0.140 864 Planarity : 0.004 0.043 1003 Dihedral : 6.082 58.874 774 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.04 % Allowed : 19.09 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.68 (0.31), residues: 701 helix: -2.02 (0.67), residues: 55 sheet: 0.50 (0.39), residues: 182 loop : -0.64 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.017 0.001 TYR A 209 PHE 0.013 0.001 PHE A 91 TRP 0.006 0.001 TRP A 249 HIS 0.002 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 5705) covalent geometry : angle 0.47878 / 0.25 ( 7774) hydrogen bonds : bond 0.03227 / 2.12 ( 142) hydrogen bonds : angle 5.66055 / 3.90 ( 390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.2315 (OUTLIER) cc_final: 0.1693 (tm-30) REVERT: B 119 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: B 176 GLN cc_start: 0.8570 (mm110) cc_final: 0.8361 (mm-40) REVERT: C 14 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8036 (tp) REVERT: C 18 ASP cc_start: 0.8564 (m-30) cc_final: 0.8334 (m-30) REVERT: C 43 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8509 (mmm) REVERT: C 65 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8012 (mt-10) REVERT: C 124 MET cc_start: 0.8448 (mmp) cc_final: 0.8112 (mmp) REVERT: C 157 PHE cc_start: 0.7481 (m-10) cc_final: 0.7106 (m-80) REVERT: C 229 ASP cc_start: 0.7567 (m-30) cc_final: 0.7119 (p0) REVERT: A 91 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.6955 (p90) REVERT: A 136 MET cc_start: 0.5982 (tmm) cc_final: 0.5531 (tmm) REVERT: A 157 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 244 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8576 (ptmt) REVERT: A 290 MET cc_start: 0.6098 (mtm) cc_final: 0.5728 (mtp) outliers start: 37 outliers final: 26 residues processed: 111 average time/residue: 0.0593 time to fit residues: 9.2541 Evaluate side-chains 111 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 288 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120030 restraints weight = 7119.245| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.11 r_work: 0.3255 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5705 Z= 0.084 Angle : 0.437 5.376 7774 Z= 0.226 Chirality : 0.041 0.138 864 Planarity : 0.004 0.039 1003 Dihedral : 5.787 56.164 774 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.92 % Allowed : 21.70 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.59 (0.31), residues: 701 helix: -2.03 (0.62), residues: 62 sheet: 0.50 (0.38), residues: 190 loop : -0.52 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.018 0.001 TYR A 209 PHE 0.027 0.001 PHE A 74 TRP 0.005 0.001 TRP C 155 HIS 0.002 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.08 ( 5705) covalent geometry : angle 0.43701 / 0.23 ( 7774) hydrogen bonds : bond 0.02709 / 1.80 ( 142) hydrogen bonds : angle 5.25133 / 3.59 ( 390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.2352 (OUTLIER) cc_final: 0.1738 (tm-30) REVERT: B 119 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7178 (pt0) REVERT: B 176 GLN cc_start: 0.8515 (mm110) cc_final: 0.8217 (mm-40) REVERT: C 14 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7986 (tp) REVERT: C 18 ASP cc_start: 0.8565 (m-30) cc_final: 0.8338 (m-30) REVERT: C 65 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7986 (mt-10) REVERT: C 124 MET cc_start: 0.8410 (mmp) cc_final: 0.8204 (mmp) REVERT: C 157 PHE cc_start: 0.7416 (m-10) cc_final: 0.7004 (m-80) REVERT: C 229 ASP cc_start: 0.7484 (m-30) cc_final: 0.7025 (p0) REVERT: A 88 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6873 (ptpp) REVERT: A 91 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.6471 (p90) REVERT: A 136 MET cc_start: 0.6060 (tmm) cc_final: 0.5544 (tmm) REVERT: A 156 LYS cc_start: 0.8687 (mmmm) cc_final: 0.8476 (mmmm) REVERT: A 157 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: A 290 MET cc_start: 0.6089 (mtm) cc_final: 0.5727 (mtp) outliers start: 24 outliers final: 16 residues processed: 102 average time/residue: 0.0678 time to fit residues: 9.4548 Evaluate side-chains 102 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 288 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 1 optimal weight: 0.0030 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 40 optimal weight: 0.0470 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 overall best weight: 0.6690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121397 restraints weight = 7276.290| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.14 r_work: 0.3271 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5705 Z= 0.082 Angle : 0.423 5.703 7774 Z= 0.219 Chirality : 0.040 0.143 864 Planarity : 0.004 0.041 1003 Dihedral : 5.408 56.007 770 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.40 % Allowed : 20.88 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.47 (0.32), residues: 701 helix: -1.91 (0.63), residues: 62 sheet: 0.63 (0.38), residues: 190 loop : -0.47 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.019 0.001 TYR A 209 PHE 0.018 0.001 PHE A 74 TRP 0.005 0.001 TRP C 155 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.08 ( 5705) covalent geometry : angle 0.42342 / 0.22 ( 7774) hydrogen bonds : bond 0.02520 / 1.69 ( 142) hydrogen bonds : angle 4.96603 / 3.39 ( 390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.2401 (OUTLIER) cc_final: 0.1764 (tm-30) REVERT: B 119 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7133 (pt0) REVERT: C 18 ASP cc_start: 0.8564 (m-30) cc_final: 0.8334 (m-30) REVERT: C 65 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7950 (mt-10) REVERT: C 124 MET cc_start: 0.8391 (mmp) cc_final: 0.8148 (mmp) REVERT: C 157 PHE cc_start: 0.7466 (m-10) cc_final: 0.7196 (m-80) REVERT: A 91 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.6249 (p90) REVERT: A 136 MET cc_start: 0.6161 (tmm) cc_final: 0.5645 (tmm) REVERT: A 157 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: A 290 MET cc_start: 0.6063 (mtm) cc_final: 0.5675 (mtp) outliers start: 27 outliers final: 17 residues processed: 111 average time/residue: 0.0622 time to fit residues: 9.5818 Evaluate side-chains 102 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 288 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 49 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.165425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116884 restraints weight = 7210.938| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.07 r_work: 0.3202 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5705 Z= 0.166 Angle : 0.493 6.148 7774 Z= 0.252 Chirality : 0.042 0.140 864 Planarity : 0.004 0.043 1003 Dihedral : 4.984 54.604 764 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.55 % Allowed : 20.55 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.57 (0.31), residues: 701 helix: -1.87 (0.64), residues: 55 sheet: 0.49 (0.37), residues: 190 loop : -0.54 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 41 TYR 0.022 0.001 TYR A 209 PHE 0.017 0.001 PHE A 74 TRP 0.007 0.001 TRP A 249 HIS 0.002 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 5705) covalent geometry : angle 0.49272 / 0.25 ( 7774) hydrogen bonds : bond 0.02936 / 1.96 ( 142) hydrogen bonds : angle 5.20602 / 3.55 ( 390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.2475 (OUTLIER) cc_final: 0.1855 (tm-30) REVERT: B 119 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7179 (pt0) REVERT: C 14 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8018 (tp) REVERT: C 18 ASP cc_start: 0.8569 (m-30) cc_final: 0.8366 (m-30) REVERT: C 65 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8041 (mt-10) REVERT: C 124 MET cc_start: 0.8453 (mmp) cc_final: 0.8200 (mmp) REVERT: C 148 MET cc_start: 0.6045 (ppp) cc_final: 0.5645 (ppp) REVERT: C 178 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5385 (m-10) REVERT: C 229 ASP cc_start: 0.7484 (m-30) cc_final: 0.7065 (p0) REVERT: A 88 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6902 (ptpp) REVERT: A 91 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.6785 (p90) REVERT: A 136 MET cc_start: 0.5712 (tmm) cc_final: 0.5470 (tmm) REVERT: A 157 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: A 290 MET cc_start: 0.6111 (mtm) cc_final: 0.5737 (mtp) outliers start: 34 outliers final: 20 residues processed: 108 average time/residue: 0.0589 time to fit residues: 8.8428 Evaluate side-chains 110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 288 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115735 restraints weight = 7309.489| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.07 r_work: 0.3151 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5705 Z= 0.170 Angle : 0.489 6.013 7774 Z= 0.252 Chirality : 0.042 0.140 864 Planarity : 0.004 0.041 1003 Dihedral : 4.970 56.194 763 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.22 % Allowed : 21.70 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.63 (0.31), residues: 701 helix: -1.91 (0.65), residues: 55 sheet: 0.43 (0.37), residues: 193 loop : -0.59 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 104 TYR 0.020 0.001 TYR A 209 PHE 0.016 0.001 PHE A 74 TRP 0.006 0.001 TRP A 249 HIS 0.002 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 5705) covalent geometry : angle 0.48854 / 0.25 ( 7774) hydrogen bonds : bond 0.02933 / 1.95 ( 142) hydrogen bonds : angle 5.24049 / 3.58 ( 390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: B 26 GLN cc_start: 0.2611 (OUTLIER) cc_final: 0.2026 (tm-30) REVERT: B 119 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7042 (pt0) REVERT: B 176 GLN cc_start: 0.8446 (mm110) cc_final: 0.8073 (mm-40) REVERT: C 14 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7977 (tp) REVERT: C 18 ASP cc_start: 0.8585 (m-30) cc_final: 0.8382 (m-30) REVERT: C 65 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7890 (mt-10) REVERT: C 124 MET cc_start: 0.8448 (mmp) cc_final: 0.8172 (mmp) REVERT: C 229 ASP cc_start: 0.7531 (m-30) cc_final: 0.7027 (p0) REVERT: A 88 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6880 (ptpp) REVERT: A 91 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.6825 (p90) REVERT: A 136 MET cc_start: 0.5750 (tmm) cc_final: 0.5461 (tmm) REVERT: A 157 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: A 290 MET cc_start: 0.5994 (mtm) cc_final: 0.5633 (mtp) outliers start: 32 outliers final: 25 residues processed: 101 average time/residue: 0.0563 time to fit residues: 7.8670 Evaluate side-chains 108 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 288 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 2 optimal weight: 7.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.167183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118323 restraints weight = 7177.306| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.10 r_work: 0.3240 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5705 Z= 0.093 Angle : 0.449 6.025 7774 Z= 0.232 Chirality : 0.041 0.138 864 Planarity : 0.004 0.039 1003 Dihedral : 4.824 56.472 763 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.22 % Allowed : 22.02 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.54 (0.31), residues: 701 helix: -1.90 (0.69), residues: 54 sheet: 0.44 (0.37), residues: 189 loop : -0.49 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.020 0.001 TYR A 209 PHE 0.015 0.001 PHE A 74 TRP 0.005 0.001 TRP A 249 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.09 ( 5705) covalent geometry : angle 0.44898 / 0.23 ( 7774) hydrogen bonds : bond 0.02740 / 1.88 ( 142) hydrogen bonds : angle 5.03423 / 3.43 ( 390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 26 GLN cc_start: 0.2567 (OUTLIER) cc_final: 0.1943 (tm-30) REVERT: B 119 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7168 (pt0) REVERT: B 129 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8370 (mm-30) REVERT: C 14 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8067 (tp) REVERT: C 18 ASP cc_start: 0.8541 (m-30) cc_final: 0.8340 (m-30) REVERT: C 43 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8512 (mmm) REVERT: C 65 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7999 (mt-10) REVERT: C 229 ASP cc_start: 0.7510 (m-30) cc_final: 0.7100 (p0) REVERT: A 88 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6848 (ptpp) REVERT: A 91 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.6614 (p90) REVERT: A 136 MET cc_start: 0.5722 (tmm) cc_final: 0.5454 (tmm) REVERT: A 157 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: A 290 MET cc_start: 0.6102 (mtm) cc_final: 0.5742 (mtp) outliers start: 32 outliers final: 23 residues processed: 102 average time/residue: 0.0591 time to fit residues: 8.2682 Evaluate side-chains 111 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 288 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114941 restraints weight = 7219.784| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.08 r_work: 0.3145 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5705 Z= 0.183 Angle : 0.515 9.948 7774 Z= 0.263 Chirality : 0.042 0.140 864 Planarity : 0.004 0.044 1003 Dihedral : 5.047 55.939 763 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 6.04 % Allowed : 21.53 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.61 (0.32), residues: 701 helix: -1.89 (0.70), residues: 53 sheet: 0.42 (0.37), residues: 193 loop : -0.58 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.023 0.002 TYR A 209 PHE 0.016 0.002 PHE A 91 TRP 0.006 0.001 TRP A 249 HIS 0.002 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 ( 5705) covalent geometry : angle 0.51490 / 0.26 ( 7774) hydrogen bonds : bond 0.03081 / 2.08 ( 142) hydrogen bonds : angle 5.33748 / 3.61 ( 390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 91 MET cc_start: 0.4556 (ptt) cc_final: 0.4343 (ttt) REVERT: B 119 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: C 14 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8014 (tp) REVERT: C 18 ASP cc_start: 0.8596 (m-30) cc_final: 0.8390 (m-30) REVERT: C 65 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7885 (mt-10) REVERT: C 178 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.5413 (m-10) REVERT: C 229 ASP cc_start: 0.7571 (m-30) cc_final: 0.7085 (p0) REVERT: A 88 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6855 (ptpp) REVERT: A 91 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.6900 (p90) REVERT: A 157 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: A 290 MET cc_start: 0.5991 (mtm) cc_final: 0.5638 (mtp) outliers start: 37 outliers final: 25 residues processed: 111 average time/residue: 0.0597 time to fit residues: 9.0843 Evaluate side-chains 114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 288 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 40.0000 chunk 25 optimal weight: 0.0970 chunk 29 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 37 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116033 restraints weight = 7233.816| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.04 r_work: 0.3156 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5705 Z= 0.153 Angle : 0.493 7.774 7774 Z= 0.253 Chirality : 0.042 0.140 864 Planarity : 0.004 0.040 1003 Dihedral : 4.188 22.317 760 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.73 % Allowed : 22.51 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.66 (0.31), residues: 701 helix: -1.93 (0.69), residues: 54 sheet: 0.39 (0.37), residues: 193 loop : -0.61 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.022 0.001 TYR A 209 PHE 0.013 0.001 PHE A 74 TRP 0.005 0.001 TRP A 249 HIS 0.002 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 5705) covalent geometry : angle 0.49305 / 0.25 ( 7774) hydrogen bonds : bond 0.02947 / 1.99 ( 142) hydrogen bonds : angle 5.19210 / 3.53 ( 390) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.149 Fit side-chains REVERT: B 72 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 91 MET cc_start: 0.4611 (ptt) cc_final: 0.4192 (ttm) REVERT: B 119 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7063 (pt0) REVERT: B 129 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8417 (mm-30) REVERT: B 176 GLN cc_start: 0.8478 (mm110) cc_final: 0.8092 (mm-40) REVERT: C 14 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7993 (tp) REVERT: C 65 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7889 (mt-10) REVERT: C 124 MET cc_start: 0.8443 (mmp) cc_final: 0.7889 (mtp) REVERT: C 229 ASP cc_start: 0.7608 (m-30) cc_final: 0.7119 (p0) REVERT: A 88 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6836 (ptpp) REVERT: A 91 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.6856 (p90) REVERT: A 157 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: A 290 MET cc_start: 0.5997 (mtm) cc_final: 0.5652 (mtp) outliers start: 29 outliers final: 22 residues processed: 106 average time/residue: 0.0575 time to fit residues: 8.4463 Evaluate side-chains 110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 288 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 0.0020 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 0.0070 chunk 50 optimal weight: 4.9990 overall best weight: 0.2606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.171127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122671 restraints weight = 7171.977| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.11 r_work: 0.3279 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5705 Z= 0.079 Angle : 0.459 6.264 7774 Z= 0.237 Chirality : 0.041 0.137 864 Planarity : 0.004 0.038 1003 Dihedral : 3.871 21.562 760 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.26 % Allowed : 23.82 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.52 (0.32), residues: 701 helix: -1.79 (0.70), residues: 54 sheet: 0.48 (0.37), residues: 193 loop : -0.51 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 151 TYR 0.021 0.001 TYR A 209 PHE 0.015 0.001 PHE B 117 TRP 0.007 0.001 TRP B 207 HIS 0.003 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.08 ( 5705) covalent geometry : angle 0.45887 / 0.24 ( 7774) hydrogen bonds : bond 0.02539 / 1.74 ( 142) hydrogen bonds : angle 4.81863 / 3.26 ( 390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1333.83 seconds wall clock time: 23 minutes 39.52 seconds (1419.52 seconds total)