Starting phenix.real_space_refine on Wed Jun 3 23:19:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r1u_53515/06_2026/9r1u_53515.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r1u_53515/06_2026/9r1u_53515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r1u_53515/06_2026/9r1u_53515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r1u_53515/06_2026/9r1u_53515.map" model { file = "/net/cci-nas-00/data/ceres_data/9r1u_53515/06_2026/9r1u_53515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r1u_53515/06_2026/9r1u_53515.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5778 2.51 5 N 1416 2.21 5 O 1536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8794 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2206 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2196 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2196 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2196 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 2.22, per 1000 atoms: 0.25 Number of scatterers: 8794 At special positions: 0 Unit cell: (121.03, 119.21, 81.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1536 8.00 N 1416 7.00 C 5778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 356.6 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 116 through 126 removed outlier: 3.616A pdb=" N VAL A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 167 Proline residue: A 161 - end of helix removed outlier: 3.732A pdb=" N PHE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.619A pdb=" N VAL A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 7.250A pdb=" N VAL A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A 225 " --> pdb=" O TRP A 221 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 289 removed outlier: 4.183A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.637A pdb=" N LEU B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.762A pdb=" N VAL B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 167 Proline residue: B 161 - end of helix removed outlier: 3.726A pdb=" N PHE B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.504A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 196 " --> pdb=" O MET B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 removed outlier: 7.234A pdb=" N VAL B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP B 225 " --> pdb=" O TRP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 289 removed outlier: 4.223A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.833A pdb=" N VAL C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 167 Proline residue: C 161 - end of helix removed outlier: 3.801A pdb=" N PHE C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.510A pdb=" N PHE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 196 " --> pdb=" O MET C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 230 removed outlier: 7.231A pdb=" N VAL C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP C 225 " --> pdb=" O TRP C 221 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 230 " --> pdb=" O PHE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 289 removed outlier: 4.068A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'D' and resid 107 through 114 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.934A pdb=" N VAL D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 167 Proline residue: D 161 - end of helix removed outlier: 3.646A pdb=" N PHE D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 196 removed outlier: 4.096A pdb=" N ASP D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 289 removed outlier: 4.065A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 335 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 removed outlier: 3.670A pdb=" N LEU D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1890 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: 1.32 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2730 1.34 - 1.46: 2276 1.46 - 1.58: 3896 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 9022 Sorted by residual: bond pdb=" CB TRP D 281 " pdb=" CG TRP D 281 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.52e+00 bond pdb=" CG MET D 153 " pdb=" SD MET D 153 " ideal model delta sigma weight residual 1.803 1.766 0.037 2.50e-02 1.60e+03 2.18e+00 bond pdb=" CB LYS B 261 " pdb=" CG LYS B 261 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CB LYS A 261 " pdb=" CG LYS A 261 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CA VAL B 319 " pdb=" CB VAL B 319 " ideal model delta sigma weight residual 1.537 1.532 0.005 5.00e-03 4.00e+04 1.04e+00 ... (remaining 9017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 12108 2.68 - 5.36: 143 5.36 - 8.04: 40 8.04 - 10.72: 15 10.72 - 13.40: 1 Bond angle restraints: 12307 Sorted by residual: angle pdb=" N PRO C 104 " pdb=" CA PRO C 104 " pdb=" CB PRO C 104 " ideal model delta sigma weight residual 103.25 111.16 -7.91 1.05e+00 9.07e-01 5.68e+01 angle pdb=" N PRO B 104 " pdb=" CA PRO B 104 " pdb=" CB PRO B 104 " ideal model delta sigma weight residual 103.25 110.95 -7.70 1.05e+00 9.07e-01 5.38e+01 angle pdb=" N PRO D 104 " pdb=" CA PRO D 104 " pdb=" CB PRO D 104 " ideal model delta sigma weight residual 103.25 110.84 -7.59 1.05e+00 9.07e-01 5.23e+01 angle pdb=" N PRO A 104 " pdb=" CA PRO A 104 " pdb=" CB PRO A 104 " ideal model delta sigma weight residual 103.52 110.11 -6.59 1.06e+00 8.90e-01 3.86e+01 angle pdb=" C MET D 152 " pdb=" N MET D 153 " pdb=" CA MET D 153 " ideal model delta sigma weight residual 122.38 114.19 8.19 1.81e+00 3.05e-01 2.05e+01 ... (remaining 12302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 4338 15.19 - 30.37: 580 30.37 - 45.56: 220 45.56 - 60.74: 53 60.74 - 75.93: 18 Dihedral angle restraints: 5209 sinusoidal: 1837 harmonic: 3372 Sorted by residual: dihedral pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" N ILE A 135 " pdb=" CA ILE A 135 " ideal model delta harmonic sigma weight residual -180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" N PRO C 104 " pdb=" C PRO C 104 " pdb=" CA PRO C 104 " pdb=" CB PRO C 104 " ideal model delta harmonic sigma weight residual 115.10 124.25 -9.15 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" N PRO D 104 " pdb=" C PRO D 104 " pdb=" CA PRO D 104 " pdb=" CB PRO D 104 " ideal model delta harmonic sigma weight residual 115.10 124.23 -9.13 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 5206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1206 0.061 - 0.122: 197 0.122 - 0.183: 11 0.183 - 0.244: 3 0.244 - 0.305: 7 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CG LEU D 377 " pdb=" CB LEU D 377 " pdb=" CD1 LEU D 377 " pdb=" CD2 LEU D 377 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CG LEU C 377 " pdb=" CB LEU C 377 " pdb=" CD1 LEU C 377 " pdb=" CD2 LEU C 377 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU A 377 " pdb=" CB LEU A 377 " pdb=" CD1 LEU A 377 " pdb=" CD2 LEU A 377 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1421 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.016 2.00e-02 2.50e+03 1.58e-02 6.28e+00 pdb=" CG TRP A 281 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 149 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C MET D 149 " 0.035 2.00e-02 2.50e+03 pdb=" O MET D 149 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU D 150 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 281 " -0.014 2.00e-02 2.50e+03 1.23e-02 3.79e+00 pdb=" CG TRP D 281 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP D 281 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP D 281 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 281 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D 281 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 281 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 281 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 281 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 281 " -0.009 2.00e-02 2.50e+03 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 443 2.72 - 3.27: 10443 3.27 - 3.81: 15753 3.81 - 4.36: 17415 4.36 - 4.90: 28212 Nonbonded interactions: 72266 Sorted by model distance: nonbonded pdb=" O ASP C 225 " pdb=" OG SER C 229 " model vdw 2.175 3.040 nonbonded pdb=" O ASP B 225 " pdb=" OG SER B 229 " model vdw 2.179 3.040 nonbonded pdb=" O ASP D 225 " pdb=" OG SER D 229 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR A 361 " pdb=" O TYR D 361 " model vdw 2.187 3.040 nonbonded pdb=" O LYS C 261 " pdb=" NZ LYS C 261 " model vdw 2.189 3.120 ... (remaining 72261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 101 through 125 or (resid 126 and (name N or name CA or na \ me C or name O or name CB )) or resid 127 or (resid 128 and (name N or name CA o \ r name C or name O or name CB )) or resid 129 through 401)) 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.570 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9022 Z= 0.145 Angle : 0.805 13.399 12307 Z= 0.410 Chirality : 0.047 0.305 1424 Planarity : 0.003 0.026 1529 Dihedral : 17.145 75.927 3017 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.69 % Favored : 92.05 % Rotamer: Outliers : 4.85 % Allowed : 32.56 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 1132 helix: 1.33 (0.18), residues: 794 sheet: None (None), residues: 0 loop : -1.50 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 258 TYR 0.030 0.002 TYR D 277 PHE 0.017 0.001 PHE A 350 TRP 0.043 0.002 TRP A 281 HIS 0.003 0.001 HIS D 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 ( 9022) covalent geometry : angle 0.80545 / 0.41 (12307) hydrogen bonds : bond 0.10066 / 6.55 ( 630) hydrogen bonds : angle 5.34408 / 3.85 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8408 (ptm160) REVERT: A 287 MET cc_start: 0.9023 (mmm) cc_final: 0.8385 (ptm) REVERT: A 381 VAL cc_start: 0.9192 (m) cc_final: 0.8981 (p) REVERT: B 138 TYR cc_start: 0.8190 (m-80) cc_final: 0.7630 (m-10) REVERT: B 263 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8220 (mt) REVERT: B 287 MET cc_start: 0.9275 (tpt) cc_final: 0.8556 (tpt) REVERT: B 381 VAL cc_start: 0.9231 (m) cc_final: 0.9021 (p) REVERT: C 138 TYR cc_start: 0.8040 (m-80) cc_final: 0.7520 (m-80) REVERT: C 273 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8319 (mmp-170) REVERT: C 381 VAL cc_start: 0.9206 (m) cc_final: 0.8973 (p) REVERT: D 113 MET cc_start: 0.9139 (ptt) cc_final: 0.8612 (ptt) REVERT: D 138 TYR cc_start: 0.8455 (m-10) cc_final: 0.7877 (m-10) REVERT: D 287 MET cc_start: 0.9095 (tpp) cc_final: 0.8231 (tpt) outliers start: 42 outliers final: 36 residues processed: 198 average time/residue: 0.0761 time to fit residues: 21.8344 Evaluate side-chains 199 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 347 TYR Chi-restraints excluded: chain D residue 361 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.078141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.063300 restraints weight = 53352.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.064581 restraints weight = 36530.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.065501 restraints weight = 27553.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.066075 restraints weight = 22312.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.066539 restraints weight = 19312.305| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9022 Z= 0.138 Angle : 0.704 10.415 12307 Z= 0.350 Chirality : 0.044 0.233 1424 Planarity : 0.004 0.039 1529 Dihedral : 8.795 58.113 1305 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.80 % Favored : 92.93 % Rotamer: Outliers : 5.77 % Allowed : 28.41 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1132 helix: 1.32 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 258 TYR 0.014 0.001 TYR B 345 PHE 0.021 0.001 PHE A 259 TRP 0.028 0.001 TRP A 281 HIS 0.001 0.000 HIS B 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 9022) covalent geometry : angle 0.70412 / 0.35 (12307) hydrogen bonds : bond 0.04428 / 3.01 ( 630) hydrogen bonds : angle 4.63731 / 3.29 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.9177 (tt) cc_final: 0.8851 (mm) REVERT: A 287 MET cc_start: 0.8987 (mmm) cc_final: 0.8430 (ptt) REVERT: A 381 VAL cc_start: 0.9235 (m) cc_final: 0.9007 (p) REVERT: B 138 TYR cc_start: 0.7939 (m-80) cc_final: 0.7712 (m-10) REVERT: B 269 LEU cc_start: 0.9192 (tt) cc_final: 0.8911 (mt) REVERT: B 276 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8291 (ptm160) REVERT: B 287 MET cc_start: 0.9259 (tpt) cc_final: 0.8517 (tpt) REVERT: B 381 VAL cc_start: 0.9244 (m) cc_final: 0.9019 (p) REVERT: C 138 TYR cc_start: 0.7873 (m-80) cc_final: 0.7547 (m-80) REVERT: C 263 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8130 (mt) REVERT: C 276 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8134 (ptm160) REVERT: C 379 MET cc_start: 0.8742 (mtt) cc_final: 0.8288 (mtt) REVERT: C 381 VAL cc_start: 0.9208 (m) cc_final: 0.8974 (p) REVERT: D 113 MET cc_start: 0.9079 (ptt) cc_final: 0.8644 (ptt) REVERT: D 192 MET cc_start: 0.9208 (pmm) cc_final: 0.8959 (pmm) REVERT: D 263 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8050 (mt) REVERT: D 276 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7636 (ttm-80) REVERT: D 287 MET cc_start: 0.9104 (tpp) cc_final: 0.8270 (tpt) REVERT: D 381 VAL cc_start: 0.9225 (m) cc_final: 0.8988 (p) outliers start: 50 outliers final: 32 residues processed: 192 average time/residue: 0.0791 time to fit residues: 22.1367 Evaluate side-chains 197 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.076488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.061624 restraints weight = 56223.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.062855 restraints weight = 38193.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.063728 restraints weight = 28594.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.064344 restraints weight = 23160.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.064735 restraints weight = 19868.117| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9022 Z= 0.199 Angle : 0.724 10.146 12307 Z= 0.367 Chirality : 0.045 0.168 1424 Planarity : 0.004 0.046 1529 Dihedral : 7.943 56.402 1268 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.89 % Favored : 92.84 % Rotamer: Outliers : 8.66 % Allowed : 27.83 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1132 helix: 1.38 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 195 TYR 0.019 0.002 TYR B 345 PHE 0.014 0.001 PHE A 259 TRP 0.019 0.002 TRP A 281 HIS 0.003 0.001 HIS C 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 ( 9022) covalent geometry : angle 0.72405 / 0.37 (12307) hydrogen bonds : bond 0.04549 / 3.04 ( 630) hydrogen bonds : angle 4.71574 / 3.35 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 160 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8239 (tp-100) REVERT: A 273 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8278 (mmp-170) REVERT: A 287 MET cc_start: 0.8975 (mmm) cc_final: 0.8421 (ptt) REVERT: A 291 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.6001 (mp) REVERT: A 368 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8372 (p) REVERT: A 381 VAL cc_start: 0.9244 (m) cc_final: 0.9006 (p) REVERT: B 138 TYR cc_start: 0.8040 (m-80) cc_final: 0.7726 (m-80) REVERT: B 276 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8208 (ptm160) REVERT: B 287 MET cc_start: 0.9241 (tpt) cc_final: 0.8533 (tpt) REVERT: B 368 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8374 (p) REVERT: B 381 VAL cc_start: 0.9266 (m) cc_final: 0.9023 (p) REVERT: C 138 TYR cc_start: 0.7936 (m-80) cc_final: 0.7567 (m-80) REVERT: C 229 SER cc_start: 0.8167 (m) cc_final: 0.7828 (t) REVERT: C 284 ILE cc_start: 0.8819 (mt) cc_final: 0.8598 (mm) REVERT: C 287 MET cc_start: 0.9192 (mmp) cc_final: 0.8797 (mmm) REVERT: C 368 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8347 (p) REVERT: C 376 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8423 (tpt) REVERT: C 381 VAL cc_start: 0.9258 (m) cc_final: 0.9023 (p) REVERT: D 113 MET cc_start: 0.9224 (ptt) cc_final: 0.8794 (ptt) REVERT: D 258 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8215 (mpp80) REVERT: D 276 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7815 (ttm-80) REVERT: D 287 MET cc_start: 0.9095 (tpp) cc_final: 0.8243 (tpt) REVERT: D 345 TYR cc_start: 0.9303 (t80) cc_final: 0.8824 (t80) REVERT: D 381 VAL cc_start: 0.9269 (m) cc_final: 0.9028 (p) outliers start: 75 outliers final: 49 residues processed: 210 average time/residue: 0.0873 time to fit residues: 25.9753 Evaluate side-chains 216 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 157 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 347 TYR Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.074630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.060215 restraints weight = 58088.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.061408 restraints weight = 39261.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.062248 restraints weight = 29449.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.062781 restraints weight = 23755.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.063171 restraints weight = 20426.343| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9022 Z= 0.264 Angle : 0.757 9.731 12307 Z= 0.396 Chirality : 0.048 0.246 1424 Planarity : 0.005 0.047 1529 Dihedral : 8.138 57.860 1264 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.80 % Favored : 92.93 % Rotamer: Outliers : 10.97 % Allowed : 27.14 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1132 helix: 1.11 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 258 TYR 0.020 0.002 TYR A 217 PHE 0.016 0.002 PHE D 350 TRP 0.035 0.002 TRP D 281 HIS 0.004 0.001 HIS C 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.26 ( 9022) covalent geometry : angle 0.75661 / 0.40 (12307) hydrogen bonds : bond 0.04837 / 3.23 ( 630) hydrogen bonds : angle 4.94221 / 3.53 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 164 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8329 (tp-100) REVERT: A 273 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8298 (mmp-170) REVERT: A 287 MET cc_start: 0.8996 (mmm) cc_final: 0.8456 (ptt) REVERT: A 368 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 381 VAL cc_start: 0.9247 (m) cc_final: 0.9004 (p) REVERT: B 263 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8309 (mt) REVERT: B 276 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8298 (ptm160) REVERT: B 287 MET cc_start: 0.9223 (tpt) cc_final: 0.8468 (tpt) REVERT: B 368 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 381 VAL cc_start: 0.9284 (m) cc_final: 0.9051 (p) REVERT: C 138 TYR cc_start: 0.8003 (m-80) cc_final: 0.7683 (m-80) REVERT: C 263 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8282 (mt) REVERT: C 284 ILE cc_start: 0.8780 (mt) cc_final: 0.8569 (mm) REVERT: C 368 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8486 (p) REVERT: C 381 VAL cc_start: 0.9283 (m) cc_final: 0.9046 (p) REVERT: D 113 MET cc_start: 0.9297 (ptt) cc_final: 0.8884 (ptt) REVERT: D 234 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: D 276 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7923 (ttm-80) REVERT: D 287 MET cc_start: 0.9065 (tpp) cc_final: 0.8246 (tpt) REVERT: D 381 VAL cc_start: 0.9280 (m) cc_final: 0.9038 (p) outliers start: 95 outliers final: 69 residues processed: 229 average time/residue: 0.0812 time to fit residues: 26.9470 Evaluate side-chains 234 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 155 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 258 ARG Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.077999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.062969 restraints weight = 54628.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.064238 restraints weight = 36725.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.065122 restraints weight = 27429.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.065705 restraints weight = 22132.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.066155 restraints weight = 19033.905| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9022 Z= 0.136 Angle : 0.736 11.324 12307 Z= 0.355 Chirality : 0.045 0.258 1424 Planarity : 0.004 0.038 1529 Dihedral : 7.886 56.036 1264 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.80 % Favored : 92.93 % Rotamer: Outliers : 7.27 % Allowed : 31.87 % Favored : 60.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1132 helix: 1.19 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -1.43 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 258 TYR 0.021 0.002 TYR B 345 PHE 0.013 0.001 PHE D 389 TRP 0.018 0.002 TRP D 281 HIS 0.002 0.000 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 9022) covalent geometry : angle 0.73617 / 0.36 (12307) hydrogen bonds : bond 0.04333 / 2.87 ( 630) hydrogen bonds : angle 4.68421 / 3.33 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7932 (tmt170) REVERT: A 276 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8579 (ptm160) REVERT: A 287 MET cc_start: 0.8954 (mmm) cc_final: 0.8431 (ptt) REVERT: A 345 TYR cc_start: 0.9266 (t80) cc_final: 0.9055 (t80) REVERT: A 368 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8272 (p) REVERT: A 381 VAL cc_start: 0.9227 (m) cc_final: 0.8995 (p) REVERT: B 276 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8351 (ptm160) REVERT: B 287 MET cc_start: 0.9226 (tpt) cc_final: 0.8487 (tpt) REVERT: B 368 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 381 VAL cc_start: 0.9238 (m) cc_final: 0.9004 (p) REVERT: C 113 MET cc_start: 0.9074 (pmm) cc_final: 0.8775 (pmm) REVERT: C 263 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8128 (mt) REVERT: C 276 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8239 (ptm160) REVERT: C 368 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8250 (p) REVERT: C 381 VAL cc_start: 0.9244 (m) cc_final: 0.9005 (p) REVERT: D 113 MET cc_start: 0.9159 (ptt) cc_final: 0.8723 (ptt) REVERT: D 276 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7705 (ttm-80) REVERT: D 287 MET cc_start: 0.9074 (tpp) cc_final: 0.8131 (tpt) REVERT: D 345 TYR cc_start: 0.9237 (t80) cc_final: 0.8498 (t80) REVERT: D 381 VAL cc_start: 0.9219 (m) cc_final: 0.8983 (p) outliers start: 63 outliers final: 42 residues processed: 204 average time/residue: 0.0833 time to fit residues: 24.4408 Evaluate side-chains 211 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 347 TYR Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.077899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.063013 restraints weight = 55360.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.064249 restraints weight = 37825.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.065130 restraints weight = 28444.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.065736 restraints weight = 23110.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.066178 restraints weight = 19841.823| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9022 Z= 0.135 Angle : 0.737 11.993 12307 Z= 0.357 Chirality : 0.045 0.275 1424 Planarity : 0.004 0.036 1529 Dihedral : 7.827 59.709 1264 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 6.47 % Allowed : 33.14 % Favored : 60.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1132 helix: 1.29 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -1.38 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 273 TYR 0.019 0.002 TYR C 277 PHE 0.013 0.001 PHE A 389 TRP 0.041 0.002 TRP D 281 HIS 0.001 0.001 HIS D 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 9022) covalent geometry : angle 0.73655 / 0.36 (12307) hydrogen bonds : bond 0.04281 / 2.83 ( 630) hydrogen bonds : angle 4.60823 / 3.28 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.9189 (tt) cc_final: 0.8879 (mt) REVERT: A 276 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8469 (ptm160) REVERT: A 287 MET cc_start: 0.8932 (mmm) cc_final: 0.8436 (ptt) REVERT: A 336 MET cc_start: 0.8880 (mmm) cc_final: 0.8613 (mmm) REVERT: A 345 TYR cc_start: 0.9261 (t80) cc_final: 0.8554 (t80) REVERT: A 368 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8215 (p) REVERT: A 381 VAL cc_start: 0.9223 (m) cc_final: 0.8975 (p) REVERT: B 273 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7628 (mmp-170) REVERT: B 287 MET cc_start: 0.9251 (tpt) cc_final: 0.8517 (tpt) REVERT: B 336 MET cc_start: 0.8895 (mmm) cc_final: 0.8638 (mpp) REVERT: B 368 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8180 (p) REVERT: B 381 VAL cc_start: 0.9241 (m) cc_final: 0.8993 (p) REVERT: C 263 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8141 (mt) REVERT: C 336 MET cc_start: 0.8847 (mmm) cc_final: 0.8618 (mpp) REVERT: C 368 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8215 (p) REVERT: C 381 VAL cc_start: 0.9241 (m) cc_final: 0.9003 (p) REVERT: D 113 MET cc_start: 0.9125 (ptt) cc_final: 0.8713 (ptt) REVERT: D 276 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7618 (ttm-80) REVERT: D 287 MET cc_start: 0.9080 (tpp) cc_final: 0.8140 (tpt) REVERT: D 381 VAL cc_start: 0.9224 (m) cc_final: 0.8983 (p) outliers start: 56 outliers final: 41 residues processed: 198 average time/residue: 0.0803 time to fit residues: 22.8549 Evaluate side-chains 207 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 347 TYR Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.076196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.061508 restraints weight = 56601.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.062715 restraints weight = 38111.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.063533 restraints weight = 28596.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.064109 restraints weight = 23239.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.064524 restraints weight = 20109.019| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9022 Z= 0.189 Angle : 0.743 11.302 12307 Z= 0.371 Chirality : 0.047 0.328 1424 Planarity : 0.004 0.041 1529 Dihedral : 7.891 57.755 1262 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.51 % Favored : 92.23 % Rotamer: Outliers : 7.39 % Allowed : 31.52 % Favored : 61.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1132 helix: 1.29 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -1.45 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 126 TYR 0.021 0.002 TYR B 345 PHE 0.012 0.001 PHE B 389 TRP 0.032 0.002 TRP D 281 HIS 0.003 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 ( 9022) covalent geometry : angle 0.74338 / 0.37 (12307) hydrogen bonds : bond 0.04458 / 2.96 ( 630) hydrogen bonds : angle 4.70235 / 3.36 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 159 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8933 (mmm) cc_final: 0.8425 (ptt) REVERT: A 345 TYR cc_start: 0.9298 (t80) cc_final: 0.8760 (t80) REVERT: A 368 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 381 VAL cc_start: 0.9244 (m) cc_final: 0.9008 (p) REVERT: B 273 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7891 (mmp-170) REVERT: B 287 MET cc_start: 0.9262 (tpt) cc_final: 0.8460 (tpt) REVERT: B 361 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: B 368 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8331 (p) REVERT: B 381 VAL cc_start: 0.9273 (m) cc_final: 0.9026 (p) REVERT: C 113 MET cc_start: 0.9060 (pmm) cc_final: 0.8794 (pmm) REVERT: C 263 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8235 (mt) REVERT: C 368 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8357 (p) REVERT: C 381 VAL cc_start: 0.9266 (m) cc_final: 0.9014 (p) REVERT: D 113 MET cc_start: 0.9225 (ptt) cc_final: 0.8762 (ptt) REVERT: D 276 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7823 (ttm-80) REVERT: D 287 MET cc_start: 0.9068 (tpp) cc_final: 0.8239 (tpt) REVERT: D 345 TYR cc_start: 0.9259 (t80) cc_final: 0.8686 (t80) REVERT: D 381 VAL cc_start: 0.9247 (m) cc_final: 0.9003 (p) outliers start: 64 outliers final: 46 residues processed: 198 average time/residue: 0.0821 time to fit residues: 23.3452 Evaluate side-chains 209 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 221 TRP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 347 TYR Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 28 optimal weight: 30.0000 chunk 56 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.076932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.062176 restraints weight = 55510.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.063376 restraints weight = 37540.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.064202 restraints weight = 28315.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.064792 restraints weight = 23092.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.065157 restraints weight = 19920.440| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9022 Z= 0.151 Angle : 0.751 11.728 12307 Z= 0.364 Chirality : 0.046 0.291 1424 Planarity : 0.004 0.035 1529 Dihedral : 7.863 59.341 1262 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.80 % Favored : 92.93 % Rotamer: Outliers : 6.12 % Allowed : 32.91 % Favored : 60.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1132 helix: 1.27 (0.18), residues: 787 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.017 0.002 TYR B 345 PHE 0.016 0.001 PHE D 350 TRP 0.028 0.002 TRP D 281 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 9022) covalent geometry : angle 0.75116 / 0.36 (12307) hydrogen bonds : bond 0.04341 / 2.87 ( 630) hydrogen bonds : angle 4.64863 / 3.31 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8433 (ptm160) REVERT: A 287 MET cc_start: 0.8930 (mmm) cc_final: 0.8457 (ptt) REVERT: A 336 MET cc_start: 0.8836 (mmm) cc_final: 0.8586 (mmm) REVERT: A 345 TYR cc_start: 0.9285 (t80) cc_final: 0.8608 (t80) REVERT: A 368 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8306 (p) REVERT: A 381 VAL cc_start: 0.9245 (m) cc_final: 0.9006 (p) REVERT: B 263 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8226 (mt) REVERT: B 273 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7904 (mmp-170) REVERT: B 276 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8426 (ptm160) REVERT: B 287 MET cc_start: 0.9222 (tpt) cc_final: 0.8477 (tpt) REVERT: B 336 MET cc_start: 0.8932 (mmm) cc_final: 0.8401 (mpp) REVERT: B 368 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8292 (p) REVERT: B 381 VAL cc_start: 0.9259 (m) cc_final: 0.9017 (p) REVERT: C 263 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8169 (mt) REVERT: C 368 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8282 (p) REVERT: C 381 VAL cc_start: 0.9260 (m) cc_final: 0.9027 (p) REVERT: D 113 MET cc_start: 0.9198 (ptt) cc_final: 0.8795 (ptt) REVERT: D 276 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7733 (ttm-80) REVERT: D 287 MET cc_start: 0.9067 (tpp) cc_final: 0.8126 (tpt) REVERT: D 345 TYR cc_start: 0.9253 (t80) cc_final: 0.8539 (t80) REVERT: D 381 VAL cc_start: 0.9248 (m) cc_final: 0.9012 (p) outliers start: 53 outliers final: 41 residues processed: 195 average time/residue: 0.0853 time to fit residues: 23.6661 Evaluate side-chains 206 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 347 TYR Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 0.0010 chunk 66 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 34 optimal weight: 0.0870 overall best weight: 0.6766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.078471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.063577 restraints weight = 54572.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.064829 restraints weight = 36926.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.065698 restraints weight = 27785.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.066302 restraints weight = 22552.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.066624 restraints weight = 19433.863| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9022 Z= 0.134 Angle : 0.762 12.820 12307 Z= 0.361 Chirality : 0.045 0.280 1424 Planarity : 0.003 0.028 1529 Dihedral : 7.751 57.717 1262 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 6.35 % Allowed : 33.03 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1132 helix: 1.34 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -1.15 (0.38), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 112 TYR 0.017 0.001 TYR B 345 PHE 0.012 0.001 PHE A 389 TRP 0.054 0.002 TRP D 281 HIS 0.001 0.000 HIS D 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9022) covalent geometry : angle 0.76241 / 0.36 (12307) hydrogen bonds : bond 0.04262 / 2.83 ( 630) hydrogen bonds : angle 4.52891 / 3.23 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8451 (ptm160) REVERT: A 287 MET cc_start: 0.8940 (mmm) cc_final: 0.8439 (ptt) REVERT: A 368 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 381 VAL cc_start: 0.9236 (m) cc_final: 0.8999 (p) REVERT: B 263 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8202 (mt) REVERT: B 276 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8388 (ptm160) REVERT: B 287 MET cc_start: 0.9227 (tpt) cc_final: 0.8498 (tpt) REVERT: B 361 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.5901 (m-80) REVERT: B 368 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8190 (p) REVERT: B 381 VAL cc_start: 0.9239 (m) cc_final: 0.9013 (p) REVERT: C 190 LEU cc_start: 0.8044 (tp) cc_final: 0.7702 (mt) REVERT: C 263 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8163 (mt) REVERT: C 368 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8179 (p) REVERT: C 381 VAL cc_start: 0.9228 (m) cc_final: 0.8974 (p) REVERT: D 113 MET cc_start: 0.9097 (ptt) cc_final: 0.8729 (ptt) REVERT: D 263 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8234 (mm) REVERT: D 276 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7706 (ttm-80) REVERT: D 287 MET cc_start: 0.9045 (tpp) cc_final: 0.8092 (tpt) REVERT: D 381 VAL cc_start: 0.9215 (m) cc_final: 0.8983 (p) outliers start: 55 outliers final: 40 residues processed: 204 average time/residue: 0.0864 time to fit residues: 25.1521 Evaluate side-chains 211 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 221 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 347 TYR Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.078663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.063798 restraints weight = 54669.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.065058 restraints weight = 37026.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.065941 restraints weight = 27811.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.066548 restraints weight = 22517.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.066828 restraints weight = 19388.882| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9022 Z= 0.138 Angle : 0.787 13.221 12307 Z= 0.373 Chirality : 0.046 0.308 1424 Planarity : 0.003 0.043 1529 Dihedral : 7.720 58.418 1260 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.24 % Favored : 92.49 % Rotamer: Outliers : 5.31 % Allowed : 34.87 % Favored : 59.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.26), residues: 1132 helix: 1.34 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 270 TYR 0.020 0.001 TYR B 345 PHE 0.012 0.001 PHE A 389 TRP 0.052 0.002 TRP D 281 HIS 0.001 0.000 HIS D 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 9022) covalent geometry : angle 0.78727 / 0.37 (12307) hydrogen bonds : bond 0.04230 / 2.81 ( 630) hydrogen bonds : angle 4.50658 / 3.20 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5249 (ttt90) REVERT: A 229 SER cc_start: 0.7852 (m) cc_final: 0.7454 (t) REVERT: A 276 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8437 (ptm160) REVERT: A 287 MET cc_start: 0.8953 (mmm) cc_final: 0.8446 (ptt) REVERT: A 350 PHE cc_start: 0.9032 (t80) cc_final: 0.8768 (t80) REVERT: A 368 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 381 VAL cc_start: 0.9217 (m) cc_final: 0.8975 (p) REVERT: B 190 LEU cc_start: 0.8018 (tp) cc_final: 0.7495 (mt) REVERT: B 263 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8201 (mt) REVERT: B 276 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8444 (ptm160) REVERT: B 287 MET cc_start: 0.9234 (tpt) cc_final: 0.8519 (tpt) REVERT: B 336 MET cc_start: 0.8855 (mmm) cc_final: 0.8599 (mpp) REVERT: B 361 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.5919 (m-80) REVERT: B 368 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8113 (p) REVERT: B 381 VAL cc_start: 0.9237 (m) cc_final: 0.9003 (p) REVERT: C 190 LEU cc_start: 0.8043 (tp) cc_final: 0.7458 (mt) REVERT: C 263 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8171 (mt) REVERT: C 368 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8120 (p) REVERT: C 381 VAL cc_start: 0.9220 (m) cc_final: 0.8990 (p) REVERT: D 113 MET cc_start: 0.9086 (ptt) cc_final: 0.8692 (ptt) REVERT: D 263 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8235 (mm) REVERT: D 276 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7665 (ttm-80) REVERT: D 287 MET cc_start: 0.9044 (tpp) cc_final: 0.8094 (tpt) REVERT: D 381 VAL cc_start: 0.9207 (m) cc_final: 0.8976 (p) outliers start: 46 outliers final: 34 residues processed: 192 average time/residue: 0.0798 time to fit residues: 22.2738 Evaluate side-chains 207 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 221 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 347 TYR Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.0060 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.078880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.064049 restraints weight = 54701.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.065367 restraints weight = 36825.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.066268 restraints weight = 27488.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.066840 restraints weight = 22164.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.067270 restraints weight = 19182.864| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9022 Z= 0.134 Angle : 0.771 13.079 12307 Z= 0.366 Chirality : 0.045 0.297 1424 Planarity : 0.003 0.027 1529 Dihedral : 7.716 58.958 1260 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.42 % Favored : 92.31 % Rotamer: Outliers : 5.66 % Allowed : 33.83 % Favored : 60.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1132 helix: 1.37 (0.18), residues: 787 sheet: None (None), residues: 0 loop : -1.17 (0.38), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 112 TYR 0.020 0.001 TYR C 138 PHE 0.011 0.001 PHE A 389 TRP 0.049 0.002 TRP D 281 HIS 0.001 0.000 HIS D 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9022) covalent geometry : angle 0.77101 / 0.37 (12307) hydrogen bonds : bond 0.04212 / 2.80 ( 630) hydrogen bonds : angle 4.43988 / 3.17 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1675.86 seconds wall clock time: 29 minutes 39.51 seconds (1779.51 seconds total)