Starting phenix.real_space_refine on Sat Dec 28 07:19:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vx3_21428/12_2024/6vx3_21428_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vx3_21428/12_2024/6vx3_21428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vx3_21428/12_2024/6vx3_21428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vx3_21428/12_2024/6vx3_21428.map" model { file = "/net/cci-nas-00/data/ceres_data/6vx3_21428/12_2024/6vx3_21428_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vx3_21428/12_2024/6vx3_21428_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 P 8 5.49 5 S 24 5.16 5 C 5336 2.51 5 N 1188 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7780 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, D Time building chain proxies: 3.70, per 1000 atoms: 0.48 Number of scatterers: 7780 At special positions: 0 Unit cell: (125.882, 125.882, 65.726, 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) S 24 16.00 P 8 15.00 O 1224 8.00 N 1188 7.00 C 5336 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 939.7 milliseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'C' and resid 24 through 43 removed outlier: 3.554A pdb=" N ILE C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 52 through 76 removed outlier: 4.310A pdb=" N ARG C 58 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 69 " --> pdb=" O TRP C 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 110 through 119 removed outlier: 3.672A pdb=" N ILE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 130 through 140 Processing helix chain 'C' and resid 146 through 166 removed outlier: 3.860A pdb=" N PHE C 155 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE C 158 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET C 164 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 165 " --> pdb=" O ILE C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 175 Processing helix chain 'C' and resid 178 through 187 removed outlier: 4.181A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 203 removed outlier: 4.109A pdb=" N ILE C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 208 through 213 removed outlier: 3.760A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 237 removed outlier: 3.576A pdb=" N PHE C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 43 removed outlier: 3.554A pdb=" N ILE A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 52 through 76 removed outlier: 4.311A pdb=" N ARG A 58 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 110 through 119 removed outlier: 3.672A pdb=" N ILE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 146 through 166 removed outlier: 3.860A pdb=" N PHE A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 178 through 187 removed outlier: 4.182A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 203 removed outlier: 4.109A pdb=" N ILE A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.760A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.576A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 43 removed outlier: 3.553A pdb=" N ILE B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 52 through 76 removed outlier: 4.310A pdb=" N ARG B 58 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 69 " --> pdb=" O TRP B 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.671A pdb=" N ILE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 146 through 166 removed outlier: 3.861A pdb=" N PHE B 155 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE B 158 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 178 through 187 removed outlier: 4.182A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 203 removed outlier: 4.109A pdb=" N ILE B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 208 through 213 removed outlier: 3.761A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.577A pdb=" N PHE B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 43 removed outlier: 3.553A pdb=" N ILE D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 52 through 76 removed outlier: 4.310A pdb=" N ARG D 58 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE D 69 " --> pdb=" O TRP D 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 103 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 110 through 119 removed outlier: 3.672A pdb=" N ILE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 130 through 140 Processing helix chain 'D' and resid 146 through 166 removed outlier: 3.860A pdb=" N PHE D 155 " --> pdb=" O MET D 151 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE D 158 " --> pdb=" O PHE D 154 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 165 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 178 through 187 removed outlier: 4.181A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 removed outlier: 4.109A pdb=" N ILE D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.760A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.577A pdb=" N PHE D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN D 234 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1032 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: 1.90 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1914 1.33 - 1.45: 1531 1.45 - 1.57: 4479 1.57 - 1.69: 16 1.69 - 1.80: 48 Bond restraints: 7988 Sorted by residual: bond pdb=" C31 POV A 301 " pdb=" O31 POV A 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C31 POV C 301 " pdb=" O31 POV C 301 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C31 POV B 301 " pdb=" O31 POV B 301 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C31 POV D 301 " pdb=" O31 POV D 301 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C31 POV A 302 " pdb=" O31 POV A 302 " ideal model delta sigma weight residual 1.327 1.451 -0.124 2.00e-02 2.50e+03 3.81e+01 ... (remaining 7983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 10241 2.05 - 4.11: 395 4.11 - 6.16: 104 6.16 - 8.21: 44 8.21 - 10.26: 20 Bond angle restraints: 10804 Sorted by residual: angle pdb=" C PHE D 67 " pdb=" N THR D 68 " pdb=" CA THR D 68 " ideal model delta sigma weight residual 120.82 127.73 -6.91 1.50e+00 4.44e-01 2.12e+01 angle pdb=" C PHE A 67 " pdb=" N THR A 68 " pdb=" CA THR A 68 " ideal model delta sigma weight residual 120.82 127.70 -6.88 1.50e+00 4.44e-01 2.10e+01 angle pdb=" C PHE C 67 " pdb=" N THR C 68 " pdb=" CA THR C 68 " ideal model delta sigma weight residual 120.82 127.69 -6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" N ILE D 59 " pdb=" CA ILE D 59 " pdb=" C ILE D 59 " ideal model delta sigma weight residual 110.72 115.33 -4.61 1.01e+00 9.80e-01 2.08e+01 angle pdb=" C PHE B 67 " pdb=" N THR B 68 " pdb=" CA THR B 68 " ideal model delta sigma weight residual 120.82 127.66 -6.84 1.50e+00 4.44e-01 2.08e+01 ... (remaining 10799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 4112 22.06 - 44.12: 436 44.12 - 66.18: 84 66.18 - 88.23: 28 88.23 - 110.29: 8 Dihedral angle restraints: 4668 sinusoidal: 2020 harmonic: 2648 Sorted by residual: dihedral pdb=" C29 POV C 301 " pdb="C210 POV C 301 " pdb="C211 POV C 301 " pdb="C212 POV C 301 " ideal model delta sinusoidal sigma weight residual 112.25 -137.46 -110.29 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" C29 POV A 301 " pdb="C210 POV A 301 " pdb="C211 POV A 301 " pdb="C212 POV A 301 " ideal model delta sinusoidal sigma weight residual 112.25 -137.46 -110.29 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" C29 POV D 301 " pdb="C210 POV D 301 " pdb="C211 POV D 301 " pdb="C212 POV D 301 " ideal model delta sinusoidal sigma weight residual 112.25 -137.47 -110.28 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 4665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 691 0.036 - 0.072: 381 0.072 - 0.108: 127 0.108 - 0.145: 21 0.145 - 0.181: 12 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CA LEU A 177 " pdb=" N LEU A 177 " pdb=" C LEU A 177 " pdb=" CB LEU A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA LEU C 177 " pdb=" N LEU C 177 " pdb=" C LEU C 177 " pdb=" CB LEU C 177 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA LEU B 177 " pdb=" N LEU B 177 " pdb=" C LEU B 177 " pdb=" CB LEU B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 1229 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 64 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.73e+00 pdb=" C LEU B 64 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU B 64 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP B 65 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 64 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C LEU D 64 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU D 64 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP D 65 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 64 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C LEU C 64 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU C 64 " -0.019 2.00e-02 2.50e+03 pdb=" N TRP C 65 " -0.017 2.00e-02 2.50e+03 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 48 2.44 - 3.06: 5553 3.06 - 3.67: 10767 3.67 - 4.29: 15929 4.29 - 4.90: 26155 Nonbonded interactions: 58452 Sorted by model distance: nonbonded pdb=" OD2 ASP D 60 " pdb=" NH2 ARG D 116 " model vdw 1.829 3.120 nonbonded pdb=" OD2 ASP A 60 " pdb=" NH2 ARG A 116 " model vdw 1.829 3.120 nonbonded pdb=" OD2 ASP C 60 " pdb=" NH2 ARG C 116 " model vdw 1.829 3.120 nonbonded pdb=" OD2 ASP B 60 " pdb=" NH2 ARG B 116 " model vdw 1.830 3.120 nonbonded pdb=" O GLN D 178 " pdb=" O32 POV D 302 " model vdw 2.014 3.040 ... (remaining 58447 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' 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 group one per residue 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: 0.590 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.730 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.009 0.127 7988 Z= 0.581 Angle : 1.110 10.264 10804 Z= 0.573 Chirality : 0.049 0.181 1232 Planarity : 0.004 0.030 1256 Dihedral : 19.669 110.293 2940 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.02 % Allowed : 10.55 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.24), residues: 892 helix: -2.22 (0.18), residues: 580 sheet: None (None), residues: 0 loop : -3.72 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 91 HIS 0.003 0.001 HIS D 22 PHE 0.023 0.002 PHE D 155 TYR 0.008 0.001 TYR C 173 ARG 0.001 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8310 (mm) REVERT: C 57 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5184 (t80) REVERT: C 191 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 224 PHE cc_start: 0.7177 (t80) cc_final: 0.6607 (t80) REVERT: C 234 ASN cc_start: 0.8423 (t0) cc_final: 0.8048 (t0) REVERT: A 48 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8334 (mm) REVERT: A 57 TYR cc_start: 0.6508 (OUTLIER) cc_final: 0.5307 (t80) REVERT: A 191 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 224 PHE cc_start: 0.7025 (t80) cc_final: 0.6623 (t80) REVERT: B 48 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8348 (mm) REVERT: B 57 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.5536 (t80) REVERT: B 63 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8594 (mm) REVERT: B 191 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8063 (tm-30) REVERT: D 48 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8320 (mm) REVERT: D 57 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5180 (t80) REVERT: D 191 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8144 (tm-30) REVERT: D 224 PHE cc_start: 0.7133 (t80) cc_final: 0.6883 (t80) outliers start: 32 outliers final: 14 residues processed: 220 average time/residue: 0.1382 time to fit residues: 44.7981 Evaluate side-chains 177 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 TRP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 0.0020 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 52 HIS B 52 HIS B 225 ASN D 52 HIS D 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7988 Z= 0.233 Angle : 0.623 8.686 10804 Z= 0.314 Chirality : 0.042 0.123 1232 Planarity : 0.003 0.023 1256 Dihedral : 20.430 112.038 1358 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.52 % Allowed : 19.60 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.25), residues: 892 helix: -1.48 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -3.30 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 54 HIS 0.005 0.002 HIS B 101 PHE 0.013 0.001 PHE B 224 TYR 0.005 0.001 TYR C 173 ARG 0.002 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 PHE cc_start: 0.8850 (t80) cc_final: 0.8503 (t80) REVERT: C 57 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.5565 (t80) REVERT: C 65 TRP cc_start: 0.5853 (OUTLIER) cc_final: 0.4345 (t60) REVERT: C 139 MET cc_start: 0.8148 (tpp) cc_final: 0.7732 (tpp) REVERT: C 191 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8353 (tm-30) REVERT: C 201 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8667 (mt) REVERT: A 35 PHE cc_start: 0.8869 (t80) cc_final: 0.8471 (t80) REVERT: A 52 HIS cc_start: 0.6412 (OUTLIER) cc_final: 0.5758 (m-70) REVERT: A 57 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.5810 (t80) REVERT: A 63 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8751 (mm) REVERT: A 65 TRP cc_start: 0.5792 (OUTLIER) cc_final: 0.4283 (t60) REVERT: A 139 MET cc_start: 0.8313 (tpp) cc_final: 0.7798 (tpp) REVERT: A 191 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 201 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8622 (mt) REVERT: B 35 PHE cc_start: 0.8759 (t80) cc_final: 0.8356 (t80) REVERT: B 52 HIS cc_start: 0.6204 (OUTLIER) cc_final: 0.5557 (m-70) REVERT: B 57 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.5663 (t80) REVERT: B 65 TRP cc_start: 0.5793 (OUTLIER) cc_final: 0.4303 (t60) REVERT: B 191 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 201 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8585 (mt) REVERT: D 35 PHE cc_start: 0.8832 (t80) cc_final: 0.8423 (t80) REVERT: D 52 HIS cc_start: 0.6291 (OUTLIER) cc_final: 0.5666 (m-70) REVERT: D 57 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.5631 (t80) REVERT: D 65 TRP cc_start: 0.5775 (OUTLIER) cc_final: 0.4261 (t60) REVERT: D 191 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8162 (tm-30) REVERT: D 201 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8583 (mt) outliers start: 36 outliers final: 17 residues processed: 199 average time/residue: 0.1608 time to fit residues: 45.8057 Evaluate side-chains 187 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 65 TRP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 54 optimal weight: 0.0470 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS A 101 HIS A 225 ASN B 101 HIS D 101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7988 Z= 0.172 Angle : 0.555 6.617 10804 Z= 0.282 Chirality : 0.040 0.105 1232 Planarity : 0.003 0.028 1256 Dihedral : 19.052 109.915 1330 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.90 % Allowed : 22.74 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.27), residues: 892 helix: -0.80 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -3.02 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 54 HIS 0.010 0.002 HIS D 52 PHE 0.014 0.001 PHE B 85 TYR 0.009 0.001 TYR C 49 ARG 0.007 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6915 (t80) REVERT: C 35 PHE cc_start: 0.8773 (t80) cc_final: 0.8430 (t80) REVERT: C 51 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7366 (p0) REVERT: C 57 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.5776 (t80) REVERT: C 59 ILE cc_start: 0.8622 (tp) cc_final: 0.8390 (tp) REVERT: C 65 TRP cc_start: 0.5988 (OUTLIER) cc_final: 0.4262 (t60) REVERT: C 138 VAL cc_start: 0.9473 (p) cc_final: 0.9172 (m) REVERT: C 139 MET cc_start: 0.8221 (tpp) cc_final: 0.7706 (tpp) REVERT: C 191 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8190 (tm-30) REVERT: C 201 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8641 (mt) REVERT: C 224 PHE cc_start: 0.6270 (t80) cc_final: 0.5603 (t80) REVERT: A 27 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.7060 (t80) REVERT: A 57 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5764 (t80) REVERT: A 65 TRP cc_start: 0.5909 (OUTLIER) cc_final: 0.4238 (t60) REVERT: A 138 VAL cc_start: 0.9446 (p) cc_final: 0.9167 (m) REVERT: A 139 MET cc_start: 0.8350 (tpp) cc_final: 0.7771 (tpp) REVERT: A 191 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 201 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 27 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7066 (t80) REVERT: B 57 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.5732 (t80) REVERT: B 59 ILE cc_start: 0.8604 (tp) cc_final: 0.8337 (tp) REVERT: B 63 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8708 (mm) REVERT: B 65 TRP cc_start: 0.5964 (OUTLIER) cc_final: 0.4278 (t60) REVERT: B 138 VAL cc_start: 0.9461 (p) cc_final: 0.9145 (m) REVERT: B 191 GLU cc_start: 0.8605 (tm-30) cc_final: 0.7900 (tm-30) REVERT: B 201 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8567 (mt) REVERT: B 224 PHE cc_start: 0.6101 (t80) cc_final: 0.5520 (t80) REVERT: D 35 PHE cc_start: 0.8768 (t80) cc_final: 0.8373 (t80) REVERT: D 57 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.5767 (t80) REVERT: D 59 ILE cc_start: 0.8653 (tp) cc_final: 0.8388 (tp) REVERT: D 63 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8767 (mm) REVERT: D 65 TRP cc_start: 0.5958 (OUTLIER) cc_final: 0.4202 (t60) REVERT: D 132 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.8035 (mtm-85) REVERT: D 138 VAL cc_start: 0.9483 (p) cc_final: 0.9154 (m) REVERT: D 139 MET cc_start: 0.8286 (tpp) cc_final: 0.7731 (tpp) REVERT: D 191 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8007 (tm-30) REVERT: D 201 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8616 (mt) outliers start: 39 outliers final: 19 residues processed: 215 average time/residue: 0.1872 time to fit residues: 55.5742 Evaluate side-chains 212 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 65 TRP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7988 Z= 0.202 Angle : 0.549 6.563 10804 Z= 0.277 Chirality : 0.040 0.113 1232 Planarity : 0.003 0.027 1256 Dihedral : 18.175 103.309 1328 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 7.54 % Allowed : 23.12 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.28), residues: 892 helix: -0.52 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -2.80 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 54 HIS 0.002 0.001 HIS A 52 PHE 0.014 0.001 PHE A 224 TYR 0.014 0.001 TYR C 49 ARG 0.011 0.001 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 PHE cc_start: 0.8770 (t80) cc_final: 0.8421 (t80) REVERT: C 57 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.5878 (t80) REVERT: C 59 ILE cc_start: 0.8251 (tp) cc_final: 0.8008 (tp) REVERT: C 65 TRP cc_start: 0.6576 (OUTLIER) cc_final: 0.4628 (t60) REVERT: C 139 MET cc_start: 0.8306 (tpp) cc_final: 0.7886 (tpp) REVERT: C 190 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7930 (mm) REVERT: C 191 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 224 PHE cc_start: 0.6272 (t80) cc_final: 0.5603 (t80) REVERT: A 57 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.5953 (t80) REVERT: A 65 TRP cc_start: 0.6508 (OUTLIER) cc_final: 0.4530 (t60) REVERT: A 138 VAL cc_start: 0.9445 (p) cc_final: 0.9115 (m) REVERT: A 139 MET cc_start: 0.8477 (tpp) cc_final: 0.7876 (tpp) REVERT: A 191 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 224 PHE cc_start: 0.5959 (t80) cc_final: 0.5470 (t80) REVERT: B 57 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.5831 (t80) REVERT: B 59 ILE cc_start: 0.8230 (tp) cc_final: 0.7881 (tp) REVERT: B 63 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8764 (mm) REVERT: B 65 TRP cc_start: 0.6476 (OUTLIER) cc_final: 0.4555 (t60) REVERT: B 138 VAL cc_start: 0.9440 (p) cc_final: 0.9130 (m) REVERT: B 139 MET cc_start: 0.8246 (tpp) cc_final: 0.7950 (tpp) REVERT: B 191 GLU cc_start: 0.8562 (tm-30) cc_final: 0.7957 (tm-30) REVERT: B 224 PHE cc_start: 0.6169 (t80) cc_final: 0.5532 (t80) REVERT: D 35 PHE cc_start: 0.8734 (t80) cc_final: 0.8266 (t80) REVERT: D 57 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.5846 (t80) REVERT: D 59 ILE cc_start: 0.8510 (tp) cc_final: 0.8202 (tp) REVERT: D 63 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8809 (mm) REVERT: D 65 TRP cc_start: 0.6552 (OUTLIER) cc_final: 0.4593 (t60) REVERT: D 139 MET cc_start: 0.8392 (tpp) cc_final: 0.7926 (tpp) REVERT: D 191 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8021 (tm-30) REVERT: D 224 PHE cc_start: 0.5989 (t80) cc_final: 0.5473 (t80) outliers start: 60 outliers final: 35 residues processed: 218 average time/residue: 0.1632 time to fit residues: 49.8383 Evaluate side-chains 226 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 65 TRP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 0.0070 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS C 225 ASN A 101 HIS A 225 ASN B 101 HIS B 225 ASN D 101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7988 Z= 0.153 Angle : 0.557 8.358 10804 Z= 0.274 Chirality : 0.040 0.138 1232 Planarity : 0.003 0.028 1256 Dihedral : 17.551 95.150 1328 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 6.91 % Allowed : 25.38 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.28), residues: 892 helix: -0.35 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -2.86 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 54 HIS 0.001 0.000 HIS C 22 PHE 0.016 0.001 PHE B 215 TYR 0.009 0.001 TYR C 49 ARG 0.007 0.001 ARG D 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 PHE cc_start: 0.8801 (t80) cc_final: 0.8509 (t80) REVERT: C 57 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.5916 (t80) REVERT: C 59 ILE cc_start: 0.8268 (tp) cc_final: 0.7987 (tp) REVERT: C 65 TRP cc_start: 0.6810 (OUTLIER) cc_final: 0.4859 (t60) REVERT: C 139 MET cc_start: 0.8323 (tpp) cc_final: 0.7959 (tpp) REVERT: C 191 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 224 PHE cc_start: 0.6187 (t80) cc_final: 0.5532 (t80) REVERT: C 230 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8809 (p) REVERT: A 57 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6030 (t80) REVERT: A 65 TRP cc_start: 0.6719 (OUTLIER) cc_final: 0.4761 (t60) REVERT: A 139 MET cc_start: 0.8472 (tpp) cc_final: 0.7942 (tpp) REVERT: A 191 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 224 PHE cc_start: 0.5890 (t80) cc_final: 0.5405 (t80) REVERT: A 230 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8822 (p) REVERT: B 57 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.5758 (t80) REVERT: B 63 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8796 (mm) REVERT: B 65 TRP cc_start: 0.6768 (OUTLIER) cc_final: 0.4872 (t60) REVERT: B 138 VAL cc_start: 0.9493 (p) cc_final: 0.9174 (m) REVERT: B 191 GLU cc_start: 0.8585 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 224 PHE cc_start: 0.6026 (t80) cc_final: 0.5423 (t80) REVERT: B 230 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8773 (p) REVERT: D 35 PHE cc_start: 0.8792 (t80) cc_final: 0.8454 (t80) REVERT: D 57 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.5857 (t80) REVERT: D 63 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8841 (mm) REVERT: D 65 TRP cc_start: 0.6795 (OUTLIER) cc_final: 0.4867 (t60) REVERT: D 139 MET cc_start: 0.8373 (tpp) cc_final: 0.7918 (tpp) REVERT: D 191 GLU cc_start: 0.8616 (tm-30) cc_final: 0.7993 (tm-30) REVERT: D 224 PHE cc_start: 0.5983 (t80) cc_final: 0.5450 (t80) REVERT: D 230 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8639 (p) outliers start: 55 outliers final: 34 residues processed: 220 average time/residue: 0.1523 time to fit residues: 47.9854 Evaluate side-chains 227 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 65 TRP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 chunk 85 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 225 ASN D 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7988 Z= 0.140 Angle : 0.540 7.627 10804 Z= 0.264 Chirality : 0.039 0.142 1232 Planarity : 0.003 0.032 1256 Dihedral : 16.895 89.519 1328 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 7.29 % Allowed : 26.63 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.28), residues: 892 helix: -0.29 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -3.00 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 54 HIS 0.001 0.000 HIS C 22 PHE 0.019 0.001 PHE B 215 TYR 0.008 0.001 TYR C 49 ARG 0.008 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 198 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ILE cc_start: 0.4233 (OUTLIER) cc_final: 0.3708 (mt) REVERT: C 35 PHE cc_start: 0.8707 (t80) cc_final: 0.8342 (t80) REVERT: C 57 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.5884 (t80) REVERT: C 139 MET cc_start: 0.8258 (tpp) cc_final: 0.7915 (tpp) REVERT: C 191 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8204 (tm-30) REVERT: C 224 PHE cc_start: 0.6130 (t80) cc_final: 0.5495 (t80) REVERT: C 230 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8737 (p) REVERT: A 19 ILE cc_start: 0.4268 (OUTLIER) cc_final: 0.3572 (mm) REVERT: A 57 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6045 (t80) REVERT: A 139 MET cc_start: 0.8439 (tpp) cc_final: 0.7955 (tpp) REVERT: A 187 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8863 (p) REVERT: A 191 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 224 PHE cc_start: 0.5766 (t80) cc_final: 0.5307 (t80) REVERT: A 230 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8755 (p) REVERT: B 19 ILE cc_start: 0.4208 (OUTLIER) cc_final: 0.3675 (mt) REVERT: B 35 PHE cc_start: 0.8782 (t80) cc_final: 0.8428 (t80) REVERT: B 57 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6003 (t80) REVERT: B 63 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8725 (mm) REVERT: B 139 MET cc_start: 0.8287 (tpp) cc_final: 0.7992 (tpp) REVERT: B 187 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8906 (p) REVERT: B 191 GLU cc_start: 0.8569 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 224 PHE cc_start: 0.6014 (t80) cc_final: 0.5391 (t80) REVERT: B 230 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8688 (p) REVERT: D 19 ILE cc_start: 0.4099 (OUTLIER) cc_final: 0.3528 (mt) REVERT: D 35 PHE cc_start: 0.8718 (t80) cc_final: 0.8358 (t80) REVERT: D 57 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.5979 (t80) REVERT: D 63 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8840 (mm) REVERT: D 139 MET cc_start: 0.8383 (tpp) cc_final: 0.7942 (tpp) REVERT: D 191 GLU cc_start: 0.8629 (tm-30) cc_final: 0.7960 (tm-30) REVERT: D 224 PHE cc_start: 0.5981 (t80) cc_final: 0.5481 (t80) REVERT: D 230 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8587 (p) outliers start: 58 outliers final: 33 residues processed: 223 average time/residue: 0.1519 time to fit residues: 49.0391 Evaluate side-chains 222 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7988 Z= 0.234 Angle : 0.581 7.570 10804 Z= 0.285 Chirality : 0.042 0.180 1232 Planarity : 0.003 0.036 1256 Dihedral : 16.396 88.793 1320 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 8.92 % Allowed : 25.75 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.28), residues: 892 helix: -0.51 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.68 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 54 HIS 0.002 0.001 HIS B 101 PHE 0.020 0.001 PHE B 215 TYR 0.007 0.001 TYR C 49 ARG 0.008 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 186 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ILE cc_start: 0.4200 (OUTLIER) cc_final: 0.3635 (mt) REVERT: C 35 PHE cc_start: 0.8757 (t80) cc_final: 0.8335 (t80) REVERT: C 57 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.5931 (t80) REVERT: C 139 MET cc_start: 0.8281 (tpp) cc_final: 0.7976 (tpp) REVERT: C 191 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8256 (tm-30) REVERT: C 224 PHE cc_start: 0.6168 (t80) cc_final: 0.5601 (t80) REVERT: A 19 ILE cc_start: 0.4321 (OUTLIER) cc_final: 0.3842 (mt) REVERT: A 57 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.5962 (t80) REVERT: A 139 MET cc_start: 0.8464 (tpp) cc_final: 0.8004 (tpp) REVERT: A 191 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 224 PHE cc_start: 0.5881 (t80) cc_final: 0.5346 (t80) REVERT: B 19 ILE cc_start: 0.4245 (OUTLIER) cc_final: 0.3708 (mt) REVERT: B 57 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.5966 (t80) REVERT: B 138 VAL cc_start: 0.9488 (p) cc_final: 0.9219 (m) REVERT: B 139 MET cc_start: 0.8377 (tpp) cc_final: 0.8077 (tpp) REVERT: B 187 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8942 (p) REVERT: B 191 GLU cc_start: 0.8657 (tm-30) cc_final: 0.7871 (tm-30) REVERT: B 224 PHE cc_start: 0.6076 (t80) cc_final: 0.5469 (t80) REVERT: D 19 ILE cc_start: 0.4144 (OUTLIER) cc_final: 0.3566 (mt) REVERT: D 35 PHE cc_start: 0.8713 (t80) cc_final: 0.8336 (t80) REVERT: D 57 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.5882 (t80) REVERT: D 191 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8034 (tm-30) REVERT: D 224 PHE cc_start: 0.6050 (t80) cc_final: 0.5567 (t80) outliers start: 71 outliers final: 41 residues processed: 223 average time/residue: 0.1436 time to fit residues: 47.2934 Evaluate side-chains 226 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7988 Z= 0.182 Angle : 0.580 7.863 10804 Z= 0.281 Chirality : 0.042 0.179 1232 Planarity : 0.003 0.036 1256 Dihedral : 16.088 89.234 1320 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 7.79 % Allowed : 28.02 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.28), residues: 892 helix: -0.32 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.71 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 54 HIS 0.001 0.000 HIS C 22 PHE 0.019 0.001 PHE C 215 TYR 0.006 0.001 TYR C 156 ARG 0.009 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ILE cc_start: 0.4121 (OUTLIER) cc_final: 0.3367 (mm) REVERT: C 35 PHE cc_start: 0.8740 (t80) cc_final: 0.8337 (t80) REVERT: C 57 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.5986 (t80) REVERT: C 139 MET cc_start: 0.8223 (tpp) cc_final: 0.7929 (tpp) REVERT: C 191 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8293 (tm-30) REVERT: C 224 PHE cc_start: 0.6149 (t80) cc_final: 0.5590 (t80) REVERT: C 230 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8722 (p) REVERT: A 19 ILE cc_start: 0.4297 (OUTLIER) cc_final: 0.3831 (mt) REVERT: A 57 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6027 (t80) REVERT: A 139 MET cc_start: 0.8432 (tpp) cc_final: 0.8025 (tpp) REVERT: A 191 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8191 (tm-30) REVERT: A 224 PHE cc_start: 0.5859 (t80) cc_final: 0.5303 (t80) REVERT: A 230 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8736 (p) REVERT: B 19 ILE cc_start: 0.4212 (OUTLIER) cc_final: 0.3686 (mt) REVERT: B 35 PHE cc_start: 0.8720 (t80) cc_final: 0.8435 (t80) REVERT: B 57 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.5855 (t80) REVERT: B 139 MET cc_start: 0.8315 (tpp) cc_final: 0.7939 (tpp) REVERT: B 187 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.8922 (p) REVERT: B 191 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8015 (tm-30) REVERT: B 224 PHE cc_start: 0.6041 (t80) cc_final: 0.5436 (t80) REVERT: B 230 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8679 (p) REVERT: D 19 ILE cc_start: 0.4156 (OUTLIER) cc_final: 0.3389 (mm) REVERT: D 35 PHE cc_start: 0.8666 (t80) cc_final: 0.8318 (t80) REVERT: D 57 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.5946 (t80) REVERT: D 139 MET cc_start: 0.8249 (tpp) cc_final: 0.7865 (tpp) REVERT: D 191 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8097 (tm-30) REVERT: D 224 PHE cc_start: 0.6029 (t80) cc_final: 0.5526 (t80) REVERT: D 230 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8614 (p) outliers start: 62 outliers final: 37 residues processed: 208 average time/residue: 0.1299 time to fit residues: 40.9667 Evaluate side-chains 225 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7988 Z= 0.190 Angle : 0.584 7.991 10804 Z= 0.286 Chirality : 0.043 0.204 1232 Planarity : 0.004 0.035 1256 Dihedral : 15.931 89.508 1320 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 7.29 % Allowed : 29.02 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.27), residues: 892 helix: -0.34 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.79 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 193 HIS 0.001 0.000 HIS C 22 PHE 0.028 0.001 PHE C 215 TYR 0.006 0.001 TYR C 49 ARG 0.008 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ILE cc_start: 0.4220 (OUTLIER) cc_final: 0.3491 (mm) REVERT: C 35 PHE cc_start: 0.8742 (t80) cc_final: 0.8331 (t80) REVERT: C 57 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.5934 (t80) REVERT: C 139 MET cc_start: 0.8212 (tpp) cc_final: 0.7920 (tpp) REVERT: C 224 PHE cc_start: 0.6166 (t80) cc_final: 0.5587 (t80) REVERT: C 230 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 19 ILE cc_start: 0.4297 (OUTLIER) cc_final: 0.3831 (mt) REVERT: A 57 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.5941 (t80) REVERT: A 139 MET cc_start: 0.8434 (tpp) cc_final: 0.8014 (tpp) REVERT: A 191 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 224 PHE cc_start: 0.5866 (t80) cc_final: 0.5314 (t80) REVERT: A 230 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8737 (p) REVERT: B 19 ILE cc_start: 0.4212 (OUTLIER) cc_final: 0.3694 (mt) REVERT: B 35 PHE cc_start: 0.8740 (t80) cc_final: 0.8405 (t80) REVERT: B 57 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.5939 (t80) REVERT: B 139 MET cc_start: 0.8427 (tpp) cc_final: 0.8027 (tpp) REVERT: B 187 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.8953 (p) REVERT: B 191 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8024 (tm-30) REVERT: B 224 PHE cc_start: 0.5941 (t80) cc_final: 0.5354 (t80) REVERT: B 230 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8681 (p) REVERT: D 19 ILE cc_start: 0.4156 (OUTLIER) cc_final: 0.3387 (mm) REVERT: D 35 PHE cc_start: 0.8667 (t80) cc_final: 0.8324 (t80) REVERT: D 57 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.5936 (t80) REVERT: D 139 MET cc_start: 0.8370 (tpp) cc_final: 0.7996 (tpp) REVERT: D 191 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8098 (tm-30) REVERT: D 224 PHE cc_start: 0.6030 (t80) cc_final: 0.5519 (t80) REVERT: D 230 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8621 (p) outliers start: 58 outliers final: 35 residues processed: 211 average time/residue: 0.1429 time to fit residues: 44.5146 Evaluate side-chains 228 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 0.0670 chunk 42 optimal weight: 0.0470 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7988 Z= 0.159 Angle : 0.592 9.976 10804 Z= 0.285 Chirality : 0.042 0.197 1232 Planarity : 0.003 0.036 1256 Dihedral : 15.568 89.931 1320 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 6.28 % Allowed : 30.15 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.28), residues: 892 helix: -0.20 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -2.66 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 193 HIS 0.001 0.000 HIS C 22 PHE 0.023 0.001 PHE D 215 TYR 0.006 0.001 TYR C 49 ARG 0.009 0.001 ARG A 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ILE cc_start: 0.4162 (OUTLIER) cc_final: 0.3453 (mm) REVERT: C 35 PHE cc_start: 0.8703 (t80) cc_final: 0.8335 (t80) REVERT: C 57 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.5947 (t80) REVERT: C 139 MET cc_start: 0.8214 (tpp) cc_final: 0.7924 (tpp) REVERT: C 224 PHE cc_start: 0.6146 (t80) cc_final: 0.5564 (t80) REVERT: C 230 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8656 (p) REVERT: A 19 ILE cc_start: 0.4252 (OUTLIER) cc_final: 0.3580 (mm) REVERT: A 57 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.5905 (t80) REVERT: A 139 MET cc_start: 0.8445 (tpp) cc_final: 0.7905 (tpp) REVERT: A 224 PHE cc_start: 0.5818 (t80) cc_final: 0.5264 (t80) REVERT: A 230 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8683 (p) REVERT: B 19 ILE cc_start: 0.4177 (OUTLIER) cc_final: 0.3658 (mt) REVERT: B 35 PHE cc_start: 0.8719 (t80) cc_final: 0.8397 (t80) REVERT: B 57 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.5905 (t80) REVERT: B 139 MET cc_start: 0.8333 (tpp) cc_final: 0.7921 (tpp) REVERT: B 191 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 224 PHE cc_start: 0.5949 (t80) cc_final: 0.5331 (t80) REVERT: B 230 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8595 (p) REVERT: D 19 ILE cc_start: 0.4342 (OUTLIER) cc_final: 0.3594 (mm) REVERT: D 35 PHE cc_start: 0.8699 (t80) cc_final: 0.8353 (t80) REVERT: D 57 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.5881 (t80) REVERT: D 139 MET cc_start: 0.8307 (tpp) cc_final: 0.7976 (tpp) REVERT: D 191 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8161 (tm-30) REVERT: D 224 PHE cc_start: 0.5948 (t80) cc_final: 0.5427 (t80) REVERT: D 230 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8550 (p) outliers start: 50 outliers final: 31 residues processed: 211 average time/residue: 0.1524 time to fit residues: 46.2875 Evaluate side-chains 221 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114296 restraints weight = 11782.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117341 restraints weight = 7074.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119349 restraints weight = 5173.950| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7988 Z= 0.201 Angle : 0.632 9.189 10804 Z= 0.302 Chirality : 0.043 0.215 1232 Planarity : 0.004 0.039 1256 Dihedral : 15.635 89.801 1320 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.78 % Allowed : 30.90 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.28), residues: 892 helix: -0.27 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.68 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 193 HIS 0.001 0.000 HIS A 22 PHE 0.021 0.001 PHE D 215 TYR 0.006 0.001 TYR C 49 ARG 0.009 0.001 ARG C 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1748.95 seconds wall clock time: 32 minutes 29.65 seconds (1949.65 seconds total)