Starting phenix.real_space_refine on Mon May 19 03:31:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g02_29642/05_2025/8g02_29642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g02_29642/05_2025/8g02_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_29642/05_2025/8g02_29642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g02_29642/05_2025/8g02_29642.map" model { file = "/net/cci-nas-00/data/ceres_data/8g02_29642/05_2025/8g02_29642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g02_29642/05_2025/8g02_29642.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.62, per 1000 atoms: 0.47 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: 5.10 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.21 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: 5.86 Time building geometry restraints manager: 6.01 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: 0.840 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: 0.290 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.180 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.058 0.002 TRP A 255 HIS 0.004 0.001 HIS A 8 PHE 0.023 0.001 PHE A 319 TYR 0.018 0.001 TYR E 176 ARG 0.009 0.001 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.15933 ( 537) hydrogen bonds : angle 5.95133 ( 1545) covalent geometry : bond 0.00289 ( 9188) covalent geometry : angle 0.61363 (12508) *********************** 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 : 1.263 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: 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: 0.5063 time to fit residues: 204.1716 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 : 1.253 ------------------------------------------------------------------------------- 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 94 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 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 = 0.4040 r_free = 0.4040 target = 0.158209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124870 restraints weight = 41357.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130132 restraints weight = 14449.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133084 restraints weight = 7373.117| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1384 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= 0.168 Angle : 0.574 6.573 12508 Z= 0.298 Chirality : 0.040 0.178 1462 Planarity : 0.006 0.117 1546 Dihedral : 4.670 43.527 1235 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.88 % Allowed : 18.27 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1136 helix: 1.09 (0.20), residues: 656 sheet: 0.38 (0.55), residues: 90 loop : -0.34 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 255 HIS 0.004 0.001 HIS A 325 PHE 0.018 0.001 PHE F 96 TYR 0.011 0.001 TYR A 97 ARG 0.007 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 537) hydrogen bonds : angle 4.75072 ( 1545) covalent geometry : bond 0.00345 ( 9188) covalent geometry : angle 0.57388 (12508) *********************** 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 337 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 319 time to evaluate : 1.265 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 307 GLN cc_start: 0.7524 (tp40) cc_final: 0.7218 (tp40) REVERT: A 329 GLU cc_start: 0.6971 (tp30) cc_final: 0.6671 (tp30) REVERT: E 74 MET cc_start: 0.7508 (mmm) cc_final: 0.7306 (mmm) REVERT: E 119 LYS cc_start: 0.8001 (tptt) cc_final: 0.7740 (tptt) REVERT: E 149 TYR cc_start: 0.8335 (t80) cc_final: 0.8006 (t80) REVERT: E 317 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.7270 (mmt90) REVERT: F 102 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7639 (tm-30) REVERT: H 77 GLN cc_start: 0.6988 (mm-40) cc_final: 0.6606 (mm110) outliers start: 18 outliers final: 13 residues processed: 323 average time/residue: 0.4864 time to fit residues: 213.6611 Evaluate side-chains 327 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 314 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 43 optimal weight: 2.9990 chunk 108 optimal weight: 0.0970 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** 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 = 0.4016 r_free = 0.4016 target = 0.156621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122207 restraints weight = 40897.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127505 restraints weight = 14168.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130513 restraints weight = 7280.169| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9188 Z= 0.155 Angle : 0.553 6.641 12508 Z= 0.284 Chirality : 0.039 0.181 1462 Planarity : 0.005 0.094 1546 Dihedral : 4.378 31.415 1232 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.57 % Allowed : 19.62 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1136 helix: 1.10 (0.20), residues: 666 sheet: 0.48 (0.52), residues: 94 loop : -0.36 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 39 HIS 0.004 0.001 HIS A 325 PHE 0.014 0.001 PHE A 253 TYR 0.009 0.001 TYR A 149 ARG 0.015 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 537) hydrogen bonds : angle 4.52563 ( 1545) covalent geometry : bond 0.00319 ( 9188) covalent geometry : angle 0.55291 (12508) *********************** 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 324 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 309 time to evaluate : 1.304 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: A 329 GLU cc_start: 0.6932 (tp30) cc_final: 0.6620 (tp30) REVERT: E 321 MET cc_start: 0.6661 (mtp) cc_final: 0.6295 (mtp) REVERT: F 102 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7707 (tm-30) outliers start: 15 outliers final: 12 residues processed: 311 average time/residue: 0.4965 time to fit residues: 208.8336 Evaluate side-chains 316 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 304 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 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 359 VAL Chi-restraints excluded: chain G residue 20 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 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 83 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.152905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119036 restraints weight = 40985.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124237 restraints weight = 14303.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127130 restraints weight = 7329.303| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9188 Z= 0.259 Angle : 0.603 6.751 12508 Z= 0.322 Chirality : 0.042 0.191 1462 Planarity : 0.005 0.081 1546 Dihedral : 4.671 28.485 1232 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.92 % Allowed : 18.79 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1136 helix: 0.81 (0.20), residues: 667 sheet: 0.21 (0.51), residues: 94 loop : -0.48 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 255 HIS 0.009 0.001 HIS A 325 PHE 0.019 0.002 PHE F 96 TYR 0.015 0.002 TYR F 71 ARG 0.006 0.001 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 537) hydrogen bonds : angle 4.65751 ( 1545) covalent geometry : bond 0.00525 ( 9188) covalent geometry : angle 0.60334 (12508) *********************** 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 358 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 330 time to evaluate : 1.309 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 36 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 197 LEU cc_start: 0.7696 (mt) cc_final: 0.7477 (mt) REVERT: A 329 GLU cc_start: 0.7057 (tp30) cc_final: 0.6748 (tp30) REVERT: E 138 SER cc_start: 0.8118 (p) cc_final: 0.7886 (p) REVERT: E 321 MET cc_start: 0.6925 (mtp) cc_final: 0.6588 (mtp) REVERT: G 55 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.5915 (mtp85) REVERT: F 102 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7750 (tm-30) outliers start: 28 outliers final: 20 residues processed: 338 average time/residue: 0.4803 time to fit residues: 220.3154 Evaluate side-chains 341 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 319 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain E residue 37 SER 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 E residue 359 VAL Chi-restraints excluded: chain B residue 5 THR 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 85 MET Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 1.9990 chunk 105 optimal weight: 0.0030 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 33 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.155248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121714 restraints weight = 41321.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.126926 restraints weight = 14287.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129888 restraints weight = 7251.059| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9188 Z= 0.129 Angle : 0.542 6.864 12508 Z= 0.276 Chirality : 0.040 0.172 1462 Planarity : 0.005 0.087 1546 Dihedral : 4.411 31.495 1232 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.19 % Allowed : 20.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1136 helix: 1.10 (0.20), residues: 668 sheet: 0.16 (0.51), residues: 94 loop : -0.42 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 39 HIS 0.003 0.001 HIS E 325 PHE 0.015 0.001 PHE A 24 TYR 0.015 0.001 TYR A 232 ARG 0.003 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 537) hydrogen bonds : angle 4.38719 ( 1545) covalent geometry : bond 0.00273 ( 9188) covalent geometry : angle 0.54226 (12508) *********************** 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 338 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 317 time to evaluate : 1.237 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 2 LEU cc_start: 0.8181 (mt) cc_final: 0.7960 (mp) REVERT: A 329 GLU cc_start: 0.6911 (tp30) cc_final: 0.6587 (tp30) REVERT: E 138 SER cc_start: 0.8124 (p) cc_final: 0.7903 (p) REVERT: G 23 LEU cc_start: 0.8418 (tp) cc_final: 0.8157 (tt) REVERT: F 102 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7682 (tm-30) outliers start: 21 outliers final: 17 residues processed: 322 average time/residue: 0.5004 time to fit residues: 217.4526 Evaluate side-chains 332 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 315 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 359 VAL 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 83 VAL Chi-restraints excluded: chain H residue 107 VAL 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 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.153007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119571 restraints weight = 41420.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124739 restraints weight = 14175.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127646 restraints weight = 7199.211| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9188 Z= 0.259 Angle : 0.599 6.729 12508 Z= 0.320 Chirality : 0.042 0.209 1462 Planarity : 0.006 0.095 1546 Dihedral : 4.705 32.420 1232 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.82 % Allowed : 20.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1136 helix: 0.86 (0.20), residues: 667 sheet: -0.03 (0.50), residues: 94 loop : -0.48 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 39 HIS 0.008 0.001 HIS A 325 PHE 0.018 0.002 PHE E 165 TYR 0.015 0.002 TYR E 176 ARG 0.008 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 537) hydrogen bonds : angle 4.58355 ( 1545) covalent geometry : bond 0.00526 ( 9188) covalent geometry : angle 0.59893 (12508) *********************** 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: 27 poor density : 322 time to evaluate : 1.317 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: A 2 LEU cc_start: 0.8228 (mt) cc_final: 0.8020 (mp) REVERT: A 36 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7830 (mt) REVERT: E 138 SER cc_start: 0.8087 (p) cc_final: 0.7853 (p) REVERT: G 23 LEU cc_start: 0.8402 (tp) cc_final: 0.8197 (tt) REVERT: G 55 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6055 (mtp85) REVERT: H 85 MET cc_start: 0.2550 (OUTLIER) cc_final: 0.2147 (pmm) REVERT: H 133 ASN cc_start: 0.2772 (OUTLIER) cc_final: 0.2338 (p0) outliers start: 27 outliers final: 22 residues processed: 331 average time/residue: 0.5075 time to fit residues: 229.3839 Evaluate side-chains 344 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 318 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain E residue 37 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 193 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 3 ARG Chi-restraints excluded: chain B residue 5 THR 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 85 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.154109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120598 restraints weight = 41205.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.125720 restraints weight = 14085.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128624 restraints weight = 7163.326| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9188 Z= 0.145 Angle : 0.551 6.843 12508 Z= 0.282 Chirality : 0.040 0.206 1462 Planarity : 0.005 0.076 1546 Dihedral : 4.494 34.640 1232 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.82 % Allowed : 21.61 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1136 helix: 1.08 (0.20), residues: 667 sheet: -0.00 (0.50), residues: 94 loop : -0.49 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 39 HIS 0.003 0.001 HIS A 325 PHE 0.017 0.001 PHE H 96 TYR 0.019 0.001 TYR A 232 ARG 0.008 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 537) hydrogen bonds : angle 4.36425 ( 1545) covalent geometry : bond 0.00302 ( 9188) covalent geometry : angle 0.55144 (12508) *********************** 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 341 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 314 time to evaluate : 1.249 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 2 LEU cc_start: 0.8189 (mt) cc_final: 0.7983 (mp) REVERT: E 138 SER cc_start: 0.7997 (p) cc_final: 0.7783 (p) REVERT: G 23 LEU cc_start: 0.8417 (tp) cc_final: 0.8207 (tt) outliers start: 27 outliers final: 21 residues processed: 321 average time/residue: 0.4988 time to fit residues: 215.7006 Evaluate side-chains 335 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 314 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 265 MET 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 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 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 83 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 100 optimal weight: 0.0870 chunk 92 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121799 restraints weight = 41134.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126933 restraints weight = 14056.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129829 restraints weight = 7135.494| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9188 Z= 0.119 Angle : 0.535 6.778 12508 Z= 0.272 Chirality : 0.040 0.197 1462 Planarity : 0.004 0.042 1546 Dihedral : 4.322 35.007 1232 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.09 % Allowed : 22.44 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1136 helix: 1.39 (0.20), residues: 653 sheet: -0.05 (0.50), residues: 94 loop : -0.43 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 39 HIS 0.004 0.001 HIS E 326 PHE 0.020 0.001 PHE H 96 TYR 0.020 0.001 TYR A 97 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 537) hydrogen bonds : angle 4.22678 ( 1545) covalent geometry : bond 0.00258 ( 9188) covalent geometry : angle 0.53524 (12508) *********************** 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 330 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 310 time to evaluate : 1.272 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: A 2 LEU cc_start: 0.8167 (mt) cc_final: 0.7962 (mp) REVERT: A 40 MET cc_start: 0.7357 (ttm) cc_final: 0.7132 (ttm) REVERT: A 329 GLU cc_start: 0.6819 (tp30) cc_final: 0.6511 (tp30) REVERT: E 17 ASN cc_start: 0.8168 (t0) cc_final: 0.7922 (t0) REVERT: E 137 MET cc_start: 0.7625 (mtp) cc_final: 0.7100 (ttp) REVERT: E 138 SER cc_start: 0.8041 (p) cc_final: 0.7817 (p) REVERT: G 23 LEU cc_start: 0.8397 (tp) cc_final: 0.8156 (tt) REVERT: G 24 LEU cc_start: 0.8579 (mt) cc_final: 0.8250 (mp) outliers start: 20 outliers final: 18 residues processed: 315 average time/residue: 0.4904 time to fit residues: 209.6583 Evaluate side-chains 325 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 307 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 265 MET 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 359 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 90 LEU Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 40.0000 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121978 restraints weight = 41172.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127137 restraints weight = 14110.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130030 restraints weight = 7128.997| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9188 Z= 0.119 Angle : 0.532 7.142 12508 Z= 0.269 Chirality : 0.039 0.157 1462 Planarity : 0.004 0.042 1546 Dihedral : 4.230 34.729 1232 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.19 % Allowed : 22.13 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1136 helix: 1.49 (0.20), residues: 653 sheet: -0.06 (0.51), residues: 94 loop : -0.35 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 39 HIS 0.004 0.001 HIS E 326 PHE 0.018 0.001 PHE H 96 TYR 0.018 0.001 TYR A 232 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 537) hydrogen bonds : angle 4.16210 ( 1545) covalent geometry : bond 0.00256 ( 9188) covalent geometry : angle 0.53234 (12508) *********************** 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 330 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 309 time to evaluate : 1.455 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 36 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7783 (mt) REVERT: A 329 GLU cc_start: 0.6836 (tp30) cc_final: 0.6534 (tp30) REVERT: E 17 ASN cc_start: 0.8182 (t0) cc_final: 0.7946 (t0) REVERT: E 53 PHE cc_start: 0.7711 (m-80) cc_final: 0.7495 (m-80) REVERT: E 138 SER cc_start: 0.8032 (p) cc_final: 0.7818 (p) REVERT: G 23 LEU cc_start: 0.8385 (tp) cc_final: 0.8148 (tt) REVERT: G 24 LEU cc_start: 0.8560 (mt) cc_final: 0.8238 (mp) outliers start: 21 outliers final: 19 residues processed: 317 average time/residue: 0.5082 time to fit residues: 220.2542 Evaluate side-chains 328 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 308 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain G residue 20 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 90 LEU Chi-restraints excluded: chain H residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 325 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 = 0.3974 r_free = 0.3974 target = 0.153187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120067 restraints weight = 41104.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125131 restraints weight = 14044.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127953 restraints weight = 7152.042| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9188 Z= 0.232 Angle : 0.581 6.770 12508 Z= 0.308 Chirality : 0.042 0.205 1462 Planarity : 0.004 0.042 1546 Dihedral : 4.548 36.624 1232 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.77 % Allowed : 22.96 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1136 helix: 1.06 (0.20), residues: 665 sheet: -0.20 (0.52), residues: 94 loop : -0.62 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 39 HIS 0.006 0.001 HIS A 325 PHE 0.015 0.001 PHE H 96 TYR 0.020 0.002 TYR A 232 ARG 0.005 0.001 ARG B 3 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 537) hydrogen bonds : angle 4.43106 ( 1545) covalent geometry : bond 0.00475 ( 9188) covalent geometry : angle 0.58114 (12508) ********************** 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 339 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 322 time to evaluate : 1.252 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 2 LEU cc_start: 0.8229 (mp) cc_final: 0.7899 (mp) REVERT: E 138 SER cc_start: 0.8094 (p) cc_final: 0.7845 (p) outliers start: 17 outliers final: 15 residues processed: 327 average time/residue: 0.4934 time to fit residues: 218.4014 Evaluate side-chains 335 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 320 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 265 MET 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 341 ARG Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain G residue 56 LEU 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 90 LEU Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 325 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 = 0.3972 r_free = 0.3972 target = 0.153283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119282 restraints weight = 40979.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124483 restraints weight = 14010.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127398 restraints weight = 7133.791| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9188 Z= 0.168 Angle : 0.562 7.137 12508 Z= 0.290 Chirality : 0.040 0.170 1462 Planarity : 0.004 0.042 1546 Dihedral : 4.482 38.834 1232 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.09 % Allowed : 23.90 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1136 helix: 1.11 (0.20), residues: 669 sheet: -0.15 (0.52), residues: 94 loop : -0.56 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 39 HIS 0.005 0.001 HIS E 326 PHE 0.024 0.001 PHE H 96 TYR 0.034 0.002 TYR E 134 ARG 0.004 0.000 ARG G 55 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 537) hydrogen bonds : angle 4.32984 ( 1545) covalent geometry : bond 0.00349 ( 9188) covalent geometry : angle 0.56169 (12508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6717.08 seconds wall clock time: 116 minutes 6.59 seconds (6966.59 seconds total)