Starting phenix.real_space_refine on Wed Aug 5 14:53:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x4h_66545/08_2026/9x4h_66545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x4h_66545/08_2026/9x4h_66545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x4h_66545/08_2026/9x4h_66545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x4h_66545/08_2026/9x4h_66545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x4h_66545/08_2026/9x4h_66545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x4h_66545/08_2026/9x4h_66545.map" } resolution = 3.36 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= -0.063 sd= 0.281 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 76 5.49 5 S 50 5.16 5 C 6088 2.51 5 N 1810 2.21 5 O 2105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10131 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2570 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "B" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1567 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain breaks: 1 Chain: "C" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1239 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 4 Chain: "D" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 633 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "E" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 576 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain breaks: 1 Chain: "F" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1917 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 238} Chain breaks: 7 Chain: "T" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1627 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 29, 'rna3p_pyr': 29} Link IDs: {'rna2p': 17, 'rna3p': 58} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.17, per 1000 atoms: 0.21 Number of scatterers: 10131 At special positions: 0 Unit cell: (76.452, 90.579, 162.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 50 16.00 P 76 15.00 O 2105 8.00 N 1810 7.00 C 6088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 322.9 milliseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2034 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 17 sheets defined 49.5% alpha, 11.0% beta 22 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 41 through 64 removed outlier: 3.511A pdb=" N THR A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A 54 " --> pdb=" O ARG A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 removed outlier: 3.919A pdb=" N TRP A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.756A pdb=" N HIS A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 4.050A pdb=" N LYS A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 206 through 220 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 230 through 254 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.503A pdb=" N GLN A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.557A pdb=" N SER A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 87 removed outlier: 3.523A pdb=" N ASP B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLN B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 127 through 148 removed outlier: 3.651A pdb=" N GLY B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 183 through 202 Processing helix chain 'B' and resid 204 through 220 removed outlier: 3.726A pdb=" N LEU B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 239 removed outlier: 3.632A pdb=" N ARG B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.978A pdb=" N GLN C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 74 removed outlier: 4.263A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 95 through 104 removed outlier: 4.260A pdb=" N SER C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU C 100 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 155 removed outlier: 3.842A pdb=" N GLY C 142 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Proline residue: C 144 - end of helix removed outlier: 4.715A pdb=" N ILE C 152 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 155 " --> pdb=" O MET C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 Processing helix chain 'D' and resid 36 through 50 removed outlier: 3.765A pdb=" N ASP D 50 " --> pdb=" O VAL D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 105 Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.726A pdb=" N ALA E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 102 removed outlier: 3.711A pdb=" N LEU E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N MET E 91 " --> pdb=" O ASN E 87 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 64 removed outlier: 4.440A pdb=" N GLN F 51 " --> pdb=" O GLN F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 102 removed outlier: 3.591A pdb=" N LEU F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 117 Processing helix chain 'F' and resid 160 through 171 removed outlier: 3.572A pdb=" N LYS F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 211 Processing helix chain 'F' and resid 230 through 248 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 276 removed outlier: 4.275A pdb=" N GLN F 272 " --> pdb=" O ASN F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 310 removed outlier: 4.423A pdb=" N MET F 300 " --> pdb=" O ASP F 296 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE F 301 " --> pdb=" O ASN F 297 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA F 310 " --> pdb=" O GLU F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 331 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 6.694A pdb=" N ILE A 18 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU A 25 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 20 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 15 removed outlier: 3.700A pdb=" N ILE A 14 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150 removed outlier: 3.511A pdb=" N LEU A 260 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 259 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 45 removed outlier: 3.500A pdb=" N CYS B 43 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 48 " --> pdb=" O TRP B 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 113 Processing sheet with id=AA9, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.674A pdb=" N LEU C 26 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AB4, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 33 removed outlier: 3.725A pdb=" N VAL E 30 " --> pdb=" O ILE E 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 23 through 26 removed outlier: 3.615A pdb=" N ARG F 20 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU F 25 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE F 18 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 23 through 26 removed outlier: 3.615A pdb=" N ARG F 20 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU F 25 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE F 18 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE F 5 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 138 through 141 423 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2994 1.34 - 1.46: 2016 1.46 - 1.58: 5197 1.58 - 1.70: 151 1.70 - 1.82: 78 Bond restraints: 10436 Sorted by residual: bond pdb=" C3' C T 29 " pdb=" O3' C T 29 " ideal model delta sigma weight residual 1.427 1.448 -0.021 1.20e-02 6.94e+03 2.97e+00 bond pdb=" C3' C T 5 " pdb=" O3' C T 5 " ideal model delta sigma weight residual 1.427 1.445 -0.018 1.20e-02 6.94e+03 2.23e+00 bond pdb=" CB PHE A 40 " pdb=" CG PHE A 40 " ideal model delta sigma weight residual 1.502 1.471 0.031 2.30e-02 1.89e+03 1.81e+00 bond pdb=" N9 A T 43 " pdb=" C4 A T 43 " ideal model delta sigma weight residual 1.374 1.366 0.008 6.00e-03 2.78e+04 1.73e+00 bond pdb=" N9 G T 7 " pdb=" C4 G T 7 " ideal model delta sigma weight residual 1.375 1.365 0.010 8.00e-03 1.56e+04 1.66e+00 ... (remaining 10431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 13811 1.75 - 3.50: 545 3.50 - 5.25: 59 5.25 - 7.00: 18 7.00 - 8.74: 3 Bond angle restraints: 14436 Sorted by residual: angle pdb=" N ILE A 155 " pdb=" CA ILE A 155 " pdb=" C ILE A 155 " ideal model delta sigma weight residual 112.98 106.74 6.24 1.25e+00 6.40e-01 2.49e+01 angle pdb=" C3' C T 5 " pdb=" O3' C T 5 " pdb=" P C T 6 " ideal model delta sigma weight residual 119.70 125.42 -5.72 1.20e+00 6.94e-01 2.27e+01 angle pdb=" O5' G T 30 " pdb=" C5' G T 30 " pdb=" C4' G T 30 " ideal model delta sigma weight residual 109.40 113.16 -3.76 8.00e-01 1.56e+00 2.21e+01 angle pdb=" O4' C T 29 " pdb=" C1' C T 29 " pdb=" N1 C T 29 " ideal model delta sigma weight residual 108.20 111.95 -3.75 8.00e-01 1.56e+00 2.20e+01 angle pdb=" C1' C T 29 " pdb=" N1 C T 29 " pdb=" C2 C T 29 " ideal model delta sigma weight residual 118.80 113.86 4.94 1.10e+00 8.26e-01 2.02e+01 ... (remaining 14431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.45: 6151 32.45 - 64.89: 311 64.89 - 97.33: 37 97.33 - 129.78: 2 129.78 - 162.22: 2 Dihedral angle restraints: 6503 sinusoidal: 3365 harmonic: 3138 Sorted by residual: dihedral pdb=" CA LYS A 171 " pdb=" C LYS A 171 " pdb=" N LEU A 172 " pdb=" CA LEU A 172 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" O4' U T 48 " pdb=" C1' U T 48 " pdb=" N1 U T 48 " pdb=" C2 U T 48 " ideal model delta sinusoidal sigma weight residual -160.00 -101.93 -58.07 1 1.50e+01 4.44e-03 2.01e+01 dihedral pdb=" CA TRP F 102 " pdb=" C TRP F 102 " pdb=" N LYS F 103 " pdb=" CA LYS F 103 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 6500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1320 0.056 - 0.111: 306 0.111 - 0.167: 104 0.167 - 0.223: 3 0.223 - 0.278: 1 Chirality restraints: 1734 Sorted by residual: chirality pdb=" C2' C T 29 " pdb=" C3' C T 29 " pdb=" O2' C T 29 " pdb=" C1' C T 29 " both_signs ideal model delta sigma weight residual False -2.60 -2.32 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA GLU A 117 " pdb=" N GLU A 117 " pdb=" C GLU A 117 " pdb=" CB GLU A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" C3' C T 5 " pdb=" C4' C T 5 " pdb=" O3' C T 5 " pdb=" C2' C T 5 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 1731 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 56 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C LEU C 56 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU C 56 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU C 57 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 40 " -0.013 2.00e-02 2.50e+03 1.38e-02 3.34e+00 pdb=" CG PHE A 40 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 40 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 40 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 40 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 40 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 104 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 105 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " 0.023 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 3304 2.85 - 3.42: 12206 3.42 - 4.00: 19781 4.00 - 4.57: 26698 4.57 - 5.14: 38242 Nonbonded interactions: 100231 Sorted by model distance: nonbonded pdb=" O2 U T 4 " pdb=" N2 G T 69 " model vdw 2.279 2.496 nonbonded pdb=" O4 U T 8 " pdb=" N7 A T 14 " model vdw 2.392 2.496 nonbonded pdb=" O PHE B 133 " pdb=" CB PHE B 137 " model vdw 2.449 2.752 nonbonded pdb=" O2' C T 29 " pdb=" OP1 G T 30 " model vdw 2.466 3.040 nonbonded pdb=" O VAL A 113 " pdb=" OE1 GLU A 117 " model vdw 2.469 3.040 ... (remaining 100226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 23 through 53 or resid 58 through 102)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 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 : 0.004 0.049 10436 Z= 0.185 Angle : 0.750 8.744 14436 Z= 0.468 Chirality : 0.052 0.278 1734 Planarity : 0.005 0.045 1557 Dihedral : 18.427 162.225 4469 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.18 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.25), residues: 1064 helix: 0.45 (0.23), residues: 473 sheet: -1.98 (0.46), residues: 135 loop : -3.13 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 55 TYR 0.013 0.002 TYR A 148 PHE 0.031 0.002 PHE A 40 TRP 0.013 0.002 TRP B 117 HIS 0.005 0.001 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (10436) covalent geometry : angle 0.74952 / 0.47 (14436) hydrogen bonds : bond 0.11561 / 7.70 ( 478) hydrogen bonds : angle 6.55267 / 4.77 ( 1321) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASN cc_start: 0.8437 (p0) cc_final: 0.7882 (p0) REVERT: A 147 ARG cc_start: 0.7709 (ttt180) cc_final: 0.7500 (ttm170) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1382 time to fit residues: 40.0334 Evaluate side-chains 182 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.143546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.128347 restraints weight = 33267.365| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.65 r_work: 0.4240 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10436 Z= 0.178 Angle : 0.726 9.396 14436 Z= 0.384 Chirality : 0.049 0.445 1734 Planarity : 0.005 0.041 1557 Dihedral : 20.070 164.300 2391 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.00 % Favored : 88.44 % Rotamer: Outliers : 1.84 % Allowed : 11.57 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.25), residues: 1064 helix: 0.38 (0.23), residues: 477 sheet: -2.05 (0.45), residues: 135 loop : -3.15 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 55 TYR 0.015 0.002 TYR A 180 PHE 0.024 0.002 PHE B 137 TRP 0.006 0.001 TRP B 117 HIS 0.004 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (10436) covalent geometry : angle 0.72594 / 0.38 (14436) hydrogen bonds : bond 0.05419 / 3.86 ( 478) hydrogen bonds : angle 5.74683 / 4.06 ( 1321) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.341 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: A 27 ASN cc_start: 0.8414 (p0) cc_final: 0.7789 (p0) REVERT: A 147 ARG cc_start: 0.7770 (ttt180) cc_final: 0.7558 (ttt180) REVERT: B 153 ASP cc_start: 0.7190 (t0) cc_final: 0.6964 (t0) REVERT: F 131 LEU cc_start: 0.8422 (tp) cc_final: 0.8015 (pp) outliers start: 17 outliers final: 10 residues processed: 192 average time/residue: 0.1276 time to fit residues: 32.6582 Evaluate side-chains 189 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 132 TYR Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 162 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 83 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.143399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.127249 restraints weight = 31988.898| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 2.76 r_work: 0.4200 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10436 Z= 0.197 Angle : 0.725 9.910 14436 Z= 0.385 Chirality : 0.048 0.466 1734 Planarity : 0.005 0.049 1557 Dihedral : 20.123 164.775 2391 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.47 % Favored : 87.97 % Rotamer: Outliers : 2.59 % Allowed : 14.59 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.25), residues: 1064 helix: 0.22 (0.23), residues: 478 sheet: -2.21 (0.44), residues: 142 loop : -3.18 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 55 TYR 0.014 0.002 TYR F 132 PHE 0.025 0.002 PHE B 137 TRP 0.008 0.002 TRP A 102 HIS 0.004 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (10436) covalent geometry : angle 0.72521 / 0.38 (14436) hydrogen bonds : bond 0.05353 / 3.84 ( 478) hydrogen bonds : angle 5.59555 / 3.95 ( 1321) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 CYS cc_start: 0.8089 (m) cc_final: 0.7342 (t) REVERT: A 27 ASN cc_start: 0.8361 (p0) cc_final: 0.7746 (p0) REVERT: A 320 THR cc_start: 0.6502 (t) cc_final: 0.5711 (p) REVERT: B 153 ASP cc_start: 0.7413 (t0) cc_final: 0.7080 (t0) REVERT: E 72 LYS cc_start: 0.8329 (mmpt) cc_final: 0.7979 (mmmt) REVERT: F 13 LYS cc_start: 0.7573 (pttt) cc_final: 0.7278 (pttp) REVERT: F 55 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7324 (mtm-85) REVERT: F 130 VAL cc_start: 0.8310 (t) cc_final: 0.7958 (p) REVERT: F 131 LEU cc_start: 0.8749 (tp) cc_final: 0.8242 (pp) REVERT: F 332 HIS cc_start: 0.7886 (t-90) cc_final: 0.7627 (t-90) outliers start: 24 outliers final: 17 residues processed: 202 average time/residue: 0.1245 time to fit residues: 33.8532 Evaluate side-chains 195 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 161 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 109 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS F 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.143876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.127316 restraints weight = 32868.492| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.87 r_work: 0.4211 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10436 Z= 0.174 Angle : 0.724 10.563 14436 Z= 0.378 Chirality : 0.048 0.474 1734 Planarity : 0.005 0.049 1557 Dihedral : 20.126 165.316 2391 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.22 % Favored : 87.31 % Rotamer: Outliers : 3.24 % Allowed : 16.76 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.25), residues: 1064 helix: 0.15 (0.23), residues: 481 sheet: -2.12 (0.44), residues: 146 loop : -3.31 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 314 TYR 0.019 0.002 TYR F 132 PHE 0.022 0.002 PHE B 137 TRP 0.009 0.001 TRP A 102 HIS 0.003 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (10436) covalent geometry : angle 0.72425 / 0.38 (14436) hydrogen bonds : bond 0.05138 / 3.69 ( 478) hydrogen bonds : angle 5.44328 / 3.83 ( 1321) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.334 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: A 3 CYS cc_start: 0.8073 (m) cc_final: 0.7342 (t) REVERT: A 27 ASN cc_start: 0.8361 (p0) cc_final: 0.7742 (p0) REVERT: A 147 ARG cc_start: 0.7901 (ttt180) cc_final: 0.7386 (ttt180) REVERT: A 320 THR cc_start: 0.6489 (t) cc_final: 0.5760 (p) REVERT: B 153 ASP cc_start: 0.7374 (t0) cc_final: 0.7015 (t0) REVERT: B 191 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6371 (mm) REVERT: E 72 LYS cc_start: 0.8254 (mmpt) cc_final: 0.7928 (mmmt) REVERT: F 13 LYS cc_start: 0.7564 (pttt) cc_final: 0.7322 (pttp) REVERT: F 130 VAL cc_start: 0.8171 (t) cc_final: 0.7855 (p) REVERT: F 131 LEU cc_start: 0.8562 (tp) cc_final: 0.8096 (pp) outliers start: 30 outliers final: 17 residues processed: 204 average time/residue: 0.1168 time to fit residues: 32.5097 Evaluate side-chains 197 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 162 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 94 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.143797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.127274 restraints weight = 32211.800| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.89 r_work: 0.4180 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10436 Z= 0.199 Angle : 0.740 10.848 14436 Z= 0.388 Chirality : 0.049 0.483 1734 Planarity : 0.005 0.051 1557 Dihedral : 20.174 165.978 2391 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.22 % Favored : 87.31 % Rotamer: Outliers : 3.03 % Allowed : 19.24 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.25), residues: 1064 helix: 0.06 (0.22), residues: 479 sheet: -2.34 (0.42), residues: 154 loop : -3.28 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 149 TYR 0.023 0.003 TYR E 24 PHE 0.024 0.002 PHE B 137 TRP 0.008 0.002 TRP A 102 HIS 0.004 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (10436) covalent geometry : angle 0.74015 / 0.39 (14436) hydrogen bonds : bond 0.05316 / 3.82 ( 478) hydrogen bonds : angle 5.45873 / 3.85 ( 1321) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.329 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: A 3 CYS cc_start: 0.8198 (m) cc_final: 0.7379 (t) REVERT: A 27 ASN cc_start: 0.8379 (p0) cc_final: 0.7753 (p0) REVERT: A 320 THR cc_start: 0.6346 (t) cc_final: 0.5653 (p) REVERT: B 153 ASP cc_start: 0.7631 (t0) cc_final: 0.7237 (t0) REVERT: B 191 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6374 (mm) REVERT: E 72 LYS cc_start: 0.8374 (mmpt) cc_final: 0.8042 (mmmt) REVERT: F 130 VAL cc_start: 0.8212 (t) cc_final: 0.7853 (p) REVERT: F 131 LEU cc_start: 0.8632 (tp) cc_final: 0.8164 (pp) outliers start: 28 outliers final: 21 residues processed: 199 average time/residue: 0.1113 time to fit residues: 29.6670 Evaluate side-chains 201 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 162 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.145185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.128560 restraints weight = 33061.551| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 2.96 r_work: 0.4179 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10436 Z= 0.176 Angle : 0.734 11.833 14436 Z= 0.383 Chirality : 0.048 0.481 1734 Planarity : 0.005 0.051 1557 Dihedral : 20.179 166.156 2391 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.22 % Favored : 87.31 % Rotamer: Outliers : 3.35 % Allowed : 20.32 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.33 (0.25), residues: 1064 helix: 0.12 (0.23), residues: 479 sheet: -2.16 (0.44), residues: 147 loop : -3.30 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 55 TYR 0.024 0.002 TYR E 24 PHE 0.029 0.002 PHE B 133 TRP 0.027 0.003 TRP B 117 HIS 0.004 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (10436) covalent geometry : angle 0.73448 / 0.38 (14436) hydrogen bonds : bond 0.05147 / 3.70 ( 478) hydrogen bonds : angle 5.36825 / 3.79 ( 1321) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.349 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: A 3 CYS cc_start: 0.8226 (m) cc_final: 0.7422 (t) REVERT: A 27 ASN cc_start: 0.8382 (p0) cc_final: 0.7760 (p0) REVERT: A 146 LYS cc_start: 0.7487 (tptp) cc_final: 0.7263 (tptp) REVERT: A 320 THR cc_start: 0.6271 (t) cc_final: 0.5598 (p) REVERT: B 153 ASP cc_start: 0.7553 (t0) cc_final: 0.7154 (t0) REVERT: B 191 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6370 (mm) REVERT: C 151 MET cc_start: 0.5617 (tmm) cc_final: 0.5306 (tmm) REVERT: F 13 LYS cc_start: 0.7342 (pttt) cc_final: 0.7060 (pttp) REVERT: F 130 VAL cc_start: 0.8219 (t) cc_final: 0.7865 (p) REVERT: F 131 LEU cc_start: 0.8678 (tp) cc_final: 0.8205 (pp) outliers start: 31 outliers final: 23 residues processed: 204 average time/residue: 0.1249 time to fit residues: 34.2532 Evaluate side-chains 207 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 295 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.143894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.126920 restraints weight = 33143.905| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 3.08 r_work: 0.4153 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10436 Z= 0.188 Angle : 0.749 11.858 14436 Z= 0.391 Chirality : 0.049 0.485 1734 Planarity : 0.005 0.052 1557 Dihedral : 20.223 166.537 2391 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.03 % Favored : 87.50 % Rotamer: Outliers : 3.57 % Allowed : 21.62 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.25), residues: 1064 helix: 0.02 (0.23), residues: 479 sheet: -2.26 (0.43), residues: 152 loop : -3.30 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 55 TYR 0.016 0.002 TYR E 24 PHE 0.022 0.002 PHE B 137 TRP 0.020 0.003 TRP B 117 HIS 0.005 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (10436) covalent geometry : angle 0.74929 / 0.39 (14436) hydrogen bonds : bond 0.05283 / 3.79 ( 478) hydrogen bonds : angle 5.40671 / 3.82 ( 1321) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.347 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: A 3 CYS cc_start: 0.8174 (m) cc_final: 0.7367 (t) REVERT: A 27 ASN cc_start: 0.8383 (p0) cc_final: 0.7753 (p0) REVERT: A 320 THR cc_start: 0.6528 (t) cc_final: 0.5927 (p) REVERT: B 75 LYS cc_start: 0.6205 (ttpt) cc_final: 0.5138 (tptt) REVERT: B 153 ASP cc_start: 0.7575 (t0) cc_final: 0.7179 (t0) REVERT: B 154 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8235 (tp) REVERT: B 191 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6369 (mm) REVERT: C 151 MET cc_start: 0.5845 (tmm) cc_final: 0.5487 (tmm) REVERT: D 68 PHE cc_start: 0.6358 (m-10) cc_final: 0.6108 (m-10) REVERT: F 13 LYS cc_start: 0.7548 (pttt) cc_final: 0.7145 (pttp) REVERT: F 130 VAL cc_start: 0.8269 (t) cc_final: 0.7910 (p) outliers start: 33 outliers final: 20 residues processed: 206 average time/residue: 0.1249 time to fit residues: 34.9169 Evaluate side-chains 205 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 162 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 10.0000 chunk 33 optimal weight: 0.0030 chunk 41 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.145448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.129121 restraints weight = 33421.714| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.79 r_work: 0.4204 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10436 Z= 0.163 Angle : 0.739 13.037 14436 Z= 0.385 Chirality : 0.047 0.479 1734 Planarity : 0.005 0.051 1557 Dihedral : 20.206 166.337 2391 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.94 % Favored : 87.59 % Rotamer: Outliers : 2.81 % Allowed : 22.81 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.25), residues: 1064 helix: 0.16 (0.23), residues: 479 sheet: -2.18 (0.44), residues: 147 loop : -3.28 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 55 TYR 0.015 0.002 TYR E 24 PHE 0.024 0.002 PHE B 133 TRP 0.020 0.002 TRP B 117 HIS 0.005 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10436) covalent geometry : angle 0.73946 / 0.39 (14436) hydrogen bonds : bond 0.05015 / 3.60 ( 478) hydrogen bonds : angle 5.31481 / 3.74 ( 1321) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.355 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: A 3 CYS cc_start: 0.8150 (m) cc_final: 0.7366 (t) REVERT: A 27 ASN cc_start: 0.8387 (p0) cc_final: 0.7733 (p0) REVERT: A 320 THR cc_start: 0.6512 (t) cc_final: 0.5966 (p) REVERT: B 75 LYS cc_start: 0.6275 (ttpt) cc_final: 0.5275 (tptt) REVERT: B 153 ASP cc_start: 0.7489 (t0) cc_final: 0.7102 (t0) REVERT: B 154 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8163 (tp) REVERT: B 191 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6463 (mm) REVERT: C 151 MET cc_start: 0.5764 (tmm) cc_final: 0.5472 (tmm) REVERT: D 68 PHE cc_start: 0.6249 (m-10) cc_final: 0.6008 (m-10) REVERT: F 16 VAL cc_start: 0.7735 (t) cc_final: 0.7403 (m) REVERT: F 70 GLU cc_start: 0.5058 (mm-30) cc_final: 0.4704 (mm-30) REVERT: F 130 VAL cc_start: 0.8201 (t) cc_final: 0.7856 (p) outliers start: 26 outliers final: 18 residues processed: 205 average time/residue: 0.1204 time to fit residues: 33.4704 Evaluate side-chains 202 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 162 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.144885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.128336 restraints weight = 32556.890| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.92 r_work: 0.4182 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10436 Z= 0.178 Angle : 0.767 13.610 14436 Z= 0.399 Chirality : 0.048 0.482 1734 Planarity : 0.005 0.051 1557 Dihedral : 20.237 166.382 2391 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.94 % Favored : 87.59 % Rotamer: Outliers : 2.70 % Allowed : 23.35 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.25), residues: 1064 helix: 0.13 (0.23), residues: 479 sheet: -2.12 (0.45), residues: 147 loop : -3.32 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 55 TYR 0.025 0.002 TYR A 180 PHE 0.023 0.002 PHE B 133 TRP 0.020 0.002 TRP A 102 HIS 0.004 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (10436) covalent geometry : angle 0.76667 / 0.40 (14436) hydrogen bonds : bond 0.05174 / 3.71 ( 478) hydrogen bonds : angle 5.35339 / 3.75 ( 1321) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 CYS cc_start: 0.8102 (m) cc_final: 0.7345 (t) REVERT: A 27 ASN cc_start: 0.8373 (p0) cc_final: 0.7730 (p0) REVERT: A 147 ARG cc_start: 0.7988 (ttt180) cc_final: 0.7641 (ttt180) REVERT: A 320 THR cc_start: 0.6609 (t) cc_final: 0.6072 (p) REVERT: B 75 LYS cc_start: 0.6345 (ttpt) cc_final: 0.5385 (tptt) REVERT: B 153 ASP cc_start: 0.7284 (t0) cc_final: 0.6946 (t0) REVERT: B 154 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8227 (tp) REVERT: B 191 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6364 (mm) REVERT: C 151 MET cc_start: 0.5882 (tmm) cc_final: 0.5543 (tmm) REVERT: D 68 PHE cc_start: 0.6364 (m-10) cc_final: 0.6097 (m-10) REVERT: F 13 LYS cc_start: 0.7464 (pttt) cc_final: 0.7015 (pttp) REVERT: F 16 VAL cc_start: 0.7819 (t) cc_final: 0.7493 (m) REVERT: F 130 VAL cc_start: 0.8194 (t) cc_final: 0.7866 (p) REVERT: F 334 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7747 (mp0) outliers start: 25 outliers final: 20 residues processed: 198 average time/residue: 0.1258 time to fit residues: 33.5076 Evaluate side-chains 201 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 162 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.144911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.128278 restraints weight = 31761.872| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 2.95 r_work: 0.4177 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10436 Z= 0.185 Angle : 0.791 14.019 14436 Z= 0.411 Chirality : 0.049 0.482 1734 Planarity : 0.005 0.059 1557 Dihedral : 20.261 166.361 2391 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.22 % Favored : 87.31 % Rotamer: Outliers : 2.49 % Allowed : 24.11 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.25), residues: 1064 helix: 0.10 (0.23), residues: 479 sheet: -2.13 (0.44), residues: 147 loop : -3.30 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 55 TYR 0.013 0.002 TYR E 24 PHE 0.021 0.002 PHE B 133 TRP 0.061 0.005 TRP B 117 HIS 0.004 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (10436) covalent geometry : angle 0.79073 / 0.41 (14436) hydrogen bonds : bond 0.05239 / 3.76 ( 478) hydrogen bonds : angle 5.39567 / 3.77 ( 1321) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 CYS cc_start: 0.8198 (m) cc_final: 0.7387 (t) REVERT: A 27 ASN cc_start: 0.8373 (p0) cc_final: 0.7714 (p0) REVERT: A 320 THR cc_start: 0.6523 (t) cc_final: 0.5993 (p) REVERT: B 75 LYS cc_start: 0.6294 (ttpt) cc_final: 0.5319 (tptt) REVERT: B 153 ASP cc_start: 0.7445 (t0) cc_final: 0.7060 (t0) REVERT: B 154 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8216 (tp) REVERT: B 186 GLU cc_start: 0.7402 (tp30) cc_final: 0.7114 (tp30) REVERT: B 191 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6411 (mm) REVERT: C 151 MET cc_start: 0.5868 (tmm) cc_final: 0.5532 (tmm) REVERT: D 68 PHE cc_start: 0.6358 (m-10) cc_final: 0.6090 (m-10) REVERT: F 13 LYS cc_start: 0.7570 (pttt) cc_final: 0.7137 (pttp) REVERT: F 16 VAL cc_start: 0.7755 (t) cc_final: 0.7456 (m) REVERT: F 130 VAL cc_start: 0.8251 (t) cc_final: 0.7890 (p) outliers start: 23 outliers final: 19 residues processed: 196 average time/residue: 0.1051 time to fit residues: 27.7484 Evaluate side-chains 200 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 162 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 0.0270 chunk 15 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 90 optimal weight: 0.0070 chunk 21 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 0.0570 chunk 59 optimal weight: 0.5980 overall best weight: 0.1574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 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 = 0.4687 r_free = 0.4687 target = 0.147388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.130971 restraints weight = 32312.294| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 3.01 r_work: 0.4228 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10436 Z= 0.155 Angle : 0.791 16.346 14436 Z= 0.404 Chirality : 0.048 0.470 1734 Planarity : 0.005 0.047 1557 Dihedral : 20.212 165.613 2391 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.56 % Favored : 87.97 % Rotamer: Outliers : 1.41 % Allowed : 25.41 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.25), residues: 1064 helix: 0.23 (0.23), residues: 485 sheet: -2.26 (0.44), residues: 142 loop : -3.26 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 55 TYR 0.015 0.002 TYR B 95 PHE 0.033 0.002 PHE B 133 TRP 0.063 0.004 TRP B 117 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (10436) covalent geometry : angle 0.79050 / 0.40 (14436) hydrogen bonds : bond 0.04801 / 3.41 ( 478) hydrogen bonds : angle 5.27727 / 3.67 ( 1321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.15 seconds wall clock time: 40 minutes 39.95 seconds (2439.95 seconds total)