Starting phenix.real_space_refine on Thu Mar 5 01:06:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g02_29642/03_2026/8g02_29642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g02_29642/03_2026/8g02_29642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g02_29642/03_2026/8g02_29642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g02_29642/03_2026/8g02_29642.map" model { file = "/net/cci-nas-00/data/ceres_data/8g02_29642/03_2026/8g02_29642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g02_29642/03_2026/8g02_29642.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 5906 2.51 5 N 1480 2.21 5 O 1536 1.98 5 H 9228 0.53 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18194 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5758 Classifications: {'peptide': 360} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 345} Chain: "E" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5758 Classifications: {'peptide': 360} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 345} Chain: "B" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1109 Classifications: {'peptide': 65} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 59} Chain: "G" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1109 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "F" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2230 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "H" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2230 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Time building chain proxies: 3.37, per 1000 atoms: 0.19 Number of scatterers: 18194 At special positions: 0 Unit cell: (89.024, 103.168, 119.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1536 8.00 N 1480 7.00 C 5906 6.00 H 9228 1.00 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: 1.65 Conformation dependent library (CDL) restraints added in 502.9 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 62.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 4.434A pdb=" N LYS A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 53 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 75 through 91 removed outlier: 4.195A pdb=" N ILE A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 121 removed outlier: 3.665A pdb=" N TRP A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 153 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.881A pdb=" N LEU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 201 through 220 removed outlier: 3.653A pdb=" N THR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 235 through 257 removed outlier: 3.629A pdb=" N LEU A 239 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 3.706A pdb=" N GLY A 269 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 334 through 360 removed outlier: 3.764A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 21 through 41 Processing helix chain 'E' and resid 42 through 53 removed outlier: 3.566A pdb=" N LEU E 51 " --> pdb=" O HIS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 91 removed outlier: 4.047A pdb=" N ILE E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 122 removed outlier: 3.737A pdb=" N TRP E 99 " --> pdb=" O ASN E 95 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 115 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.738A pdb=" N GLY E 127 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU E 128 " --> pdb=" O THR E 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 128' Processing helix chain 'E' and resid 129 through 152 removed outlier: 3.864A pdb=" N LYS E 133 " --> pdb=" O ILE E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 174 through 195 removed outlier: 3.798A pdb=" N LEU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 220 Processing helix chain 'E' and resid 221 through 229 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 238 through 258 removed outlier: 3.776A pdb=" N PHE E 256 " --> pdb=" O GLY E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 284 removed outlier: 3.731A pdb=" N GLY E 269 " --> pdb=" O MET E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 294 through 314 Processing helix chain 'E' and resid 323 through 332 removed outlier: 3.534A pdb=" N HIS E 327 " --> pdb=" O PRO E 323 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 332 " --> pdb=" O TYR E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 357 removed outlier: 3.812A pdb=" N LEU E 357 " --> pdb=" O GLY E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.511A pdb=" N THR B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) Proline residue: B 21 - end of helix removed outlier: 3.842A pdb=" N ILE B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.056A pdb=" N ARG B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 52 removed outlier: 3.541A pdb=" N ALA B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 25 Proline residue: G 21 - end of helix Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 35 through 51 Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 63 through 68 Processing helix chain 'F' and resid 143 through 149 Processing helix chain 'H' and resid 42 through 50 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 143 through 149 Processing sheet with id=AA1, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.756A pdb=" N THR F 110 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL F 118 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL F 112 " --> pdb=" O HIS F 116 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 58 removed outlier: 3.825A pdb=" N LYS G 57 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL H 118 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL H 112 " --> pdb=" O HIS H 116 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 22 through 25 removed outlier: 7.747A pdb=" N VAL F 15 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU F 25 " --> pdb=" O TYR F 13 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR F 13 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 22 through 25 removed outlier: 7.747A pdb=" N VAL F 15 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU F 25 " --> pdb=" O TYR F 13 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR F 13 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA F 138 " --> pdb=" O SER F 10 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA F 12 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL F 136 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLN F 14 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL F 134 " --> pdb=" O GLN F 14 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ARG F 16 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE F 132 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 removed outlier: 6.918A pdb=" N LEU H 22 " --> pdb=" O THR H 17 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR H 17 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP H 24 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL H 15 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 25 removed outlier: 6.918A pdb=" N LEU H 22 " --> pdb=" O THR H 17 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR H 17 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP H 24 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL H 15 " --> pdb=" O ASP H 24 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL H 8 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE H 139 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER H 10 " --> pdb=" O VAL H 137 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1545 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: 4.16 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9222 1.04 - 1.24: 1121 1.24 - 1.44: 2771 1.44 - 1.64: 5220 1.64 - 1.84: 82 Bond restraints: 18416 Sorted by residual: bond pdb=" CB MET H 85 " pdb=" CG MET H 85 " ideal model delta sigma weight residual 1.520 1.594 -0.074 3.00e-02 1.11e+03 6.15e+00 bond pdb=" N GLY G 1 " pdb=" CA GLY G 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.05e+00 bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.03e+00 bond pdb=" CG MET H 85 " pdb=" SD MET H 85 " ideal model delta sigma weight residual 1.803 1.842 -0.039 2.50e-02 1.60e+03 2.43e+00 bond pdb=" N GLY G 1 " pdb=" H GLY G 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 18411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 33274 2.52 - 5.05: 125 5.05 - 7.57: 12 7.57 - 10.09: 2 10.09 - 12.61: 1 Bond angle restraints: 33414 Sorted by residual: angle pdb=" CG MET H 85 " pdb=" SD MET H 85 " pdb=" CE MET H 85 " ideal model delta sigma weight residual 100.90 110.19 -9.29 2.20e+00 2.07e-01 1.78e+01 angle pdb=" CB MET H 85 " pdb=" CG MET H 85 " pdb=" SD MET H 85 " ideal model delta sigma weight residual 112.70 125.31 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" N MET H 85 " pdb=" CA MET H 85 " pdb=" CB MET H 85 " ideal model delta sigma weight residual 111.56 117.41 -5.85 1.58e+00 4.01e-01 1.37e+01 angle pdb=" C MET A 203 " pdb=" N PRO A 204 " pdb=" CD PRO A 204 " ideal model delta sigma weight residual 120.60 113.40 7.20 2.20e+00 2.07e-01 1.07e+01 angle pdb=" C MET A 203 " pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta sigma weight residual 127.00 134.65 -7.65 2.40e+00 1.74e-01 1.02e+01 ... (remaining 33409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 7447 17.10 - 34.19: 762 34.19 - 51.29: 266 51.29 - 68.39: 98 68.39 - 85.48: 7 Dihedral angle restraints: 8580 sinusoidal: 4602 harmonic: 3978 Sorted by residual: dihedral pdb=" CA LEU B 24 " pdb=" C LEU B 24 " pdb=" N ILE B 25 " pdb=" CA ILE B 25 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ILE A 202 " pdb=" C ILE A 202 " pdb=" N MET A 203 " pdb=" CA MET A 203 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU A 197 " pdb=" C LEU A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1040 0.035 - 0.071: 288 0.071 - 0.106: 99 0.106 - 0.142: 32 0.142 - 0.177: 3 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CB VAL A 308 " pdb=" CA VAL A 308 " pdb=" CG1 VAL A 308 " pdb=" CG2 VAL A 308 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE A 230 " pdb=" N ILE A 230 " pdb=" C ILE A 230 " pdb=" CB ILE A 230 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ARG G 55 " pdb=" N ARG G 55 " pdb=" C ARG G 55 " pdb=" CB ARG G 55 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1459 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 255 " 0.025 2.00e-02 2.50e+03 1.79e-02 1.29e+01 pdb=" CG TRP A 255 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 255 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 255 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 255 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 255 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 255 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 255 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 255 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 255 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 255 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 TRP A 255 " 0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP A 255 " -0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 255 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 255 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 255 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 55 " 0.295 9.50e-02 1.11e+02 9.88e-02 1.10e+01 pdb=" NE ARG G 55 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG G 55 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG G 55 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 55 " 0.010 2.00e-02 2.50e+03 pdb="HH11 ARG G 55 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG G 55 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG G 55 " -0.012 2.00e-02 2.50e+03 pdb="HH22 ARG G 55 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 335 " 0.049 5.00e-02 4.00e+02 7.37e-02 8.68e+00 pdb=" N PRO A 336 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.041 5.00e-02 4.00e+02 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1308 2.20 - 2.80: 38234 2.80 - 3.40: 52285 3.40 - 4.00: 65943 4.00 - 4.60: 102050 Nonbonded interactions: 259820 Sorted by model distance: nonbonded pdb=" OE1 GLU A 287 " pdb=" H GLU A 287 " model vdw 1.605 2.450 nonbonded pdb=" O MET E 40 " pdb=" H MET E 44 " model vdw 1.641 2.450 nonbonded pdb=" O LEU B 19 " pdb=" HG SER B 22 " model vdw 1.654 2.450 nonbonded pdb="HE22 GLN E 307 " pdb=" O PHE E 319 " model vdw 1.680 2.450 nonbonded pdb="HH12 ARG E 314 " pdb=" OE1 GLN E 316 " model vdw 1.681 2.450 ... (remaining 259815 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 1.180 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: 0.090 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.960 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 0.074 9188 Z= 0.130 Angle : 0.614 12.613 12508 Z= 0.312 Chirality : 0.040 0.177 1462 Planarity : 0.007 0.128 1546 Dihedral : 15.732 84.149 3236 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.10 % Allowed : 19.52 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.25), residues: 1136 helix: 1.11 (0.21), residues: 630 sheet: 0.53 (0.57), residues: 92 loop : -0.10 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 43 TYR 0.018 0.001 TYR E 176 PHE 0.023 0.001 PHE A 319 TRP 0.058 0.002 TRP A 255 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9188) covalent geometry : angle 0.61363 (12508) hydrogen bonds : bond 0.15933 ( 537) hydrogen bonds : angle 5.95133 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 0.444 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: 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 307 GLN cc_start: 0.7369 (tp40) cc_final: 0.7154 (tp40) REVERT: A 329 GLU cc_start: 0.7078 (tp30) cc_final: 0.6797 (tp30) outliers start: 1 outliers final: 1 residues processed: 296 average time/residue: 0.2387 time to fit residues: 95.8593 Evaluate side-chains 293 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.155490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121542 restraints weight = 41514.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126748 restraints weight = 14439.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.129680 restraints weight = 7444.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131308 restraints weight = 5167.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131952 restraints weight = 4295.750| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9188 Z= 0.224 Angle : 0.615 6.649 12508 Z= 0.324 Chirality : 0.041 0.188 1462 Planarity : 0.006 0.117 1546 Dihedral : 4.838 40.125 1235 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.98 % Allowed : 17.95 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.53 (0.24), residues: 1136 helix: 0.86 (0.20), residues: 660 sheet: 0.33 (0.55), residues: 90 loop : -0.38 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 42 TYR 0.012 0.002 TYR E 328 PHE 0.020 0.002 PHE F 96 TRP 0.023 0.002 TRP A 255 HIS 0.005 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 9188) covalent geometry : angle 0.61502 (12508) hydrogen bonds : bond 0.04826 ( 537) hydrogen bonds : angle 4.77469 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 326 time to evaluate : 0.450 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: 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 307 GLN cc_start: 0.7575 (tp40) cc_final: 0.7295 (tp40) REVERT: A 329 GLU cc_start: 0.7031 (tp30) cc_final: 0.6740 (tp30) REVERT: E 119 LYS cc_start: 0.8048 (tptt) cc_final: 0.7773 (tptt) REVERT: G 24 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7940 (mp) REVERT: F 102 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7722 (tm-30) REVERT: H 96 PHE cc_start: 0.6811 (m-80) cc_final: 0.6573 (m-80) outliers start: 19 outliers final: 15 residues processed: 330 average time/residue: 0.2365 time to fit residues: 106.3895 Evaluate side-chains 336 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 320 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117845 restraints weight = 41473.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122997 restraints weight = 14386.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125926 restraints weight = 7355.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127544 restraints weight = 5071.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128197 restraints weight = 4210.642| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9188 Z= 0.301 Angle : 0.639 6.906 12508 Z= 0.346 Chirality : 0.043 0.201 1462 Planarity : 0.006 0.096 1546 Dihedral : 4.969 29.154 1232 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.30 % Allowed : 19.10 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.09 (0.24), residues: 1136 helix: 0.49 (0.19), residues: 662 sheet: 0.19 (0.54), residues: 90 loop : -0.54 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 42 TYR 0.017 0.002 TYR F 71 PHE 0.020 0.002 PHE F 96 TRP 0.024 0.002 TRP B 39 HIS 0.009 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 9188) covalent geometry : angle 0.63856 (12508) hydrogen bonds : bond 0.05225 ( 537) hydrogen bonds : angle 4.87098 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 335 time to evaluate : 0.567 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.6775 (m-80) cc_final: 0.6551 (m-80) REVERT: A 244 THR cc_start: 0.8116 (p) cc_final: 0.7895 (p) REVERT: E 138 SER cc_start: 0.8109 (p) cc_final: 0.7869 (p) REVERT: E 321 MET cc_start: 0.7045 (mtp) cc_final: 0.6739 (mtp) REVERT: G 55 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6000 (mtp85) REVERT: F 14 GLN cc_start: 0.3562 (mp10) cc_final: 0.3314 (mp10) REVERT: H 96 PHE cc_start: 0.6868 (m-80) cc_final: 0.6533 (m-80) outliers start: 22 outliers final: 16 residues processed: 339 average time/residue: 0.2419 time to fit residues: 111.1860 Evaluate side-chains 344 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 327 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 0.0020 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.155376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122174 restraints weight = 41323.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127346 restraints weight = 14123.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130244 restraints weight = 7138.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131821 restraints weight = 4900.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.132505 restraints weight = 4067.214| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9188 Z= 0.149 Angle : 0.557 6.893 12508 Z= 0.287 Chirality : 0.040 0.180 1462 Planarity : 0.005 0.098 1546 Dihedral : 4.608 33.157 1232 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.77 % Allowed : 21.29 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.35 (0.24), residues: 1136 helix: 0.80 (0.20), residues: 668 sheet: 0.09 (0.51), residues: 94 loop : -0.61 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 3 TYR 0.011 0.001 TYR A 92 PHE 0.014 0.001 PHE F 96 TRP 0.018 0.001 TRP B 39 HIS 0.003 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9188) covalent geometry : angle 0.55738 (12508) hydrogen bonds : bond 0.04345 ( 537) hydrogen bonds : angle 4.50265 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 319 time to evaluate : 0.479 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8202 (mt) cc_final: 0.7978 (mp) REVERT: A 35 PHE cc_start: 0.6753 (m-80) cc_final: 0.6522 (m-80) REVERT: A 197 LEU cc_start: 0.7739 (mt) cc_final: 0.7531 (mt) REVERT: E 138 SER cc_start: 0.8075 (p) cc_final: 0.7866 (p) REVERT: E 321 MET cc_start: 0.7105 (mtp) cc_final: 0.6332 (mtp) REVERT: G 24 LEU cc_start: 0.8452 (mp) cc_final: 0.8148 (mp) REVERT: H 96 PHE cc_start: 0.6770 (m-80) cc_final: 0.6503 (m-80) outliers start: 17 outliers final: 15 residues processed: 323 average time/residue: 0.2474 time to fit residues: 107.8588 Evaluate side-chains 332 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 317 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain B residue 3 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 100 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121098 restraints weight = 40930.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126264 restraints weight = 13966.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.129154 restraints weight = 7057.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130724 restraints weight = 4857.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131441 restraints weight = 4033.832| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9188 Z= 0.145 Angle : 0.543 6.795 12508 Z= 0.280 Chirality : 0.040 0.168 1462 Planarity : 0.005 0.093 1546 Dihedral : 4.511 33.158 1232 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.92 % Allowed : 20.88 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.53 (0.25), residues: 1136 helix: 0.96 (0.20), residues: 668 sheet: 0.05 (0.50), residues: 94 loop : -0.55 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 3 TYR 0.013 0.001 TYR A 232 PHE 0.013 0.001 PHE F 96 TRP 0.015 0.001 TRP B 39 HIS 0.006 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9188) covalent geometry : angle 0.54332 (12508) hydrogen bonds : bond 0.04190 ( 537) hydrogen bonds : angle 4.40632 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 319 time to evaluate : 0.454 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: 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: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8199 (mt) cc_final: 0.7985 (mp) REVERT: E 138 SER cc_start: 0.8077 (p) cc_final: 0.7873 (p) REVERT: E 321 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6576 (mtp) REVERT: E 341 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7175 (mmt-90) REVERT: H 96 PHE cc_start: 0.6766 (m-80) cc_final: 0.6491 (m-80) outliers start: 28 outliers final: 17 residues processed: 328 average time/residue: 0.2451 time to fit residues: 108.6733 Evaluate side-chains 334 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 315 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 321 MET Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 3 ARG Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.154146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121105 restraints weight = 40748.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126234 restraints weight = 13955.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129071 restraints weight = 7045.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130646 restraints weight = 4853.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.131244 restraints weight = 4031.136| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9188 Z= 0.146 Angle : 0.542 6.802 12508 Z= 0.278 Chirality : 0.039 0.169 1462 Planarity : 0.005 0.061 1546 Dihedral : 4.430 34.370 1232 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.03 % Allowed : 20.04 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.65 (0.25), residues: 1136 helix: 1.08 (0.20), residues: 668 sheet: 0.03 (0.50), residues: 94 loop : -0.51 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 3 TYR 0.011 0.001 TYR A 232 PHE 0.017 0.001 PHE E 165 TRP 0.013 0.001 TRP B 39 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9188) covalent geometry : angle 0.54158 (12508) hydrogen bonds : bond 0.04079 ( 537) hydrogen bonds : angle 4.33380 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 320 time to evaluate : 0.392 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: 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: symmetry clash REVERT: A 2 LEU cc_start: 0.8196 (mt) cc_final: 0.7986 (mp) REVERT: A 35 PHE cc_start: 0.6778 (m-80) cc_final: 0.6530 (m-80) REVERT: A 321 MET cc_start: 0.7865 (ttm) cc_final: 0.7663 (ttm) REVERT: E 321 MET cc_start: 0.6936 (mtp) cc_final: 0.6634 (mtp) REVERT: H 96 PHE cc_start: 0.6764 (m-80) cc_final: 0.6446 (m-80) outliers start: 29 outliers final: 22 residues processed: 329 average time/residue: 0.2407 time to fit residues: 107.3979 Evaluate side-chains 337 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 315 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 TRP Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN F 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.153236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120264 restraints weight = 41165.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125311 restraints weight = 14043.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128160 restraints weight = 7145.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129691 restraints weight = 4924.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130383 restraints weight = 4099.568| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9188 Z= 0.246 Angle : 0.590 6.808 12508 Z= 0.314 Chirality : 0.042 0.183 1462 Planarity : 0.005 0.076 1546 Dihedral : 4.697 38.586 1232 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.34 % Allowed : 21.29 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.38 (0.24), residues: 1136 helix: 0.82 (0.20), residues: 672 sheet: -0.16 (0.52), residues: 90 loop : -0.51 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 285 TYR 0.019 0.002 TYR A 232 PHE 0.015 0.001 PHE E 165 TRP 0.011 0.001 TRP E 217 HIS 0.007 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9188) covalent geometry : angle 0.59026 (12508) hydrogen bonds : bond 0.04530 ( 537) hydrogen bonds : angle 4.54783 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 322 time to evaluate : 0.461 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: 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: symmetry clash REVERT: A 2 LEU cc_start: 0.8239 (mt) cc_final: 0.8029 (mp) REVERT: A 35 PHE cc_start: 0.6810 (m-80) cc_final: 0.6577 (m-80) REVERT: E 137 MET cc_start: 0.7619 (mtp) cc_final: 0.7179 (ttp) REVERT: E 175 PHE cc_start: 0.7771 (m-10) cc_final: 0.7498 (m-10) REVERT: E 321 MET cc_start: 0.6982 (mtp) cc_final: 0.6713 (mtp) REVERT: E 330 LEU cc_start: 0.8339 (mt) cc_final: 0.8098 (mm) REVERT: E 341 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7452 (mmt-90) REVERT: G 23 LEU cc_start: 0.8353 (tp) cc_final: 0.8130 (tt) REVERT: H 96 PHE cc_start: 0.6861 (m-80) cc_final: 0.6556 (m-80) outliers start: 32 outliers final: 24 residues processed: 333 average time/residue: 0.2286 time to fit residues: 103.2901 Evaluate side-chains 344 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 319 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 TRP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 87 optimal weight: 0.0870 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.154753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121895 restraints weight = 40753.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.126979 restraints weight = 13866.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.129829 restraints weight = 7028.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131277 restraints weight = 4838.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131913 restraints weight = 4050.232| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9188 Z= 0.146 Angle : 0.553 6.831 12508 Z= 0.284 Chirality : 0.040 0.180 1462 Planarity : 0.005 0.075 1546 Dihedral : 4.547 40.111 1232 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.30 % Allowed : 22.76 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1136 helix: 1.06 (0.20), residues: 668 sheet: -0.13 (0.53), residues: 90 loop : -0.54 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.019 0.001 TYR A 232 PHE 0.016 0.001 PHE A 253 TRP 0.011 0.001 TRP B 39 HIS 0.003 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9188) covalent geometry : angle 0.55275 (12508) hydrogen bonds : bond 0.04138 ( 537) hydrogen bonds : angle 4.36916 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 320 time to evaluate : 0.471 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8214 (mt) cc_final: 0.8006 (mp) REVERT: E 181 TYR cc_start: 0.8584 (t80) cc_final: 0.8012 (t80) REVERT: G 23 LEU cc_start: 0.8372 (tp) cc_final: 0.8121 (tt) REVERT: H 96 PHE cc_start: 0.6764 (m-80) cc_final: 0.6447 (m-80) outliers start: 22 outliers final: 20 residues processed: 327 average time/residue: 0.2389 time to fit residues: 105.8642 Evaluate side-chains 338 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 318 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 TRP Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.153817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120840 restraints weight = 40944.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125917 restraints weight = 13947.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128728 restraints weight = 7074.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130236 restraints weight = 4878.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130837 restraints weight = 4065.170| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9188 Z= 0.170 Angle : 0.557 6.771 12508 Z= 0.288 Chirality : 0.040 0.177 1462 Planarity : 0.005 0.070 1546 Dihedral : 4.519 39.444 1232 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.82 % Allowed : 22.23 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.58 (0.25), residues: 1136 helix: 1.04 (0.20), residues: 672 sheet: -0.16 (0.53), residues: 90 loop : -0.54 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 42 TYR 0.019 0.001 TYR A 232 PHE 0.017 0.001 PHE E 165 TRP 0.010 0.001 TRP B 39 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9188) covalent geometry : angle 0.55670 (12508) hydrogen bonds : bond 0.04172 ( 537) hydrogen bonds : angle 4.36495 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 321 time to evaluate : 0.605 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8204 (mt) cc_final: 0.7987 (mp) REVERT: A 35 PHE cc_start: 0.6805 (m-80) cc_final: 0.6547 (m-80) REVERT: E 341 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7405 (mmt-90) REVERT: G 23 LEU cc_start: 0.8358 (tp) cc_final: 0.8152 (tt) REVERT: H 96 PHE cc_start: 0.6797 (m-80) cc_final: 0.6533 (m-80) outliers start: 27 outliers final: 21 residues processed: 329 average time/residue: 0.2361 time to fit residues: 105.5402 Evaluate side-chains 340 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 318 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 TRP Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.0010 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.154093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.120918 restraints weight = 40976.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125918 restraints weight = 13949.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128787 restraints weight = 7128.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130293 restraints weight = 4923.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131080 restraints weight = 4114.354| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9188 Z= 0.173 Angle : 0.559 6.773 12508 Z= 0.289 Chirality : 0.040 0.193 1462 Planarity : 0.005 0.066 1546 Dihedral : 4.534 40.959 1232 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.30 % Allowed : 23.17 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.56 (0.25), residues: 1136 helix: 1.04 (0.20), residues: 672 sheet: -0.26 (0.53), residues: 90 loop : -0.55 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 42 TYR 0.022 0.001 TYR A 232 PHE 0.017 0.001 PHE E 165 TRP 0.010 0.001 TRP B 39 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9188) covalent geometry : angle 0.55876 (12508) hydrogen bonds : bond 0.04167 ( 537) hydrogen bonds : angle 4.37470 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 318 time to evaluate : 0.494 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: 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: symmetry clash REVERT: A 329 GLU cc_start: 0.6916 (tp30) cc_final: 0.6590 (tp30) REVERT: E 341 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7405 (mmt-90) REVERT: H 96 PHE cc_start: 0.6821 (m-80) cc_final: 0.6551 (m-80) outliers start: 22 outliers final: 18 residues processed: 325 average time/residue: 0.2390 time to fit residues: 104.8900 Evaluate side-chains 337 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 318 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 39 TRP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122014 restraints weight = 41302.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127148 restraints weight = 13830.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130041 restraints weight = 6952.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131621 restraints weight = 4777.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132229 restraints weight = 3960.660| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9188 Z= 0.182 Angle : 0.565 7.106 12508 Z= 0.292 Chirality : 0.041 0.227 1462 Planarity : 0.004 0.049 1546 Dihedral : 4.525 40.329 1232 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.40 % Allowed : 23.38 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.56 (0.25), residues: 1136 helix: 1.04 (0.20), residues: 672 sheet: -0.25 (0.53), residues: 90 loop : -0.56 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 42 TYR 0.024 0.002 TYR A 97 PHE 0.016 0.001 PHE E 165 TRP 0.010 0.001 TRP A 39 HIS 0.005 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9188) covalent geometry : angle 0.56484 (12508) hydrogen bonds : bond 0.04212 ( 537) hydrogen bonds : angle 4.39772 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3865.70 seconds wall clock time: 66 minutes 21.18 seconds (3981.18 seconds total)