Starting phenix.real_space_refine on Wed Feb 4 04:53:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1g_70006/02_2026/9o1g_70006_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1g_70006/02_2026/9o1g_70006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o1g_70006/02_2026/9o1g_70006_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1g_70006/02_2026/9o1g_70006_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o1g_70006/02_2026/9o1g_70006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1g_70006/02_2026/9o1g_70006.map" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 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 Zn 1 6.06 5 S 65 5.16 5 C 5960 2.51 5 N 1392 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8915 Number of models: 1 Model: "" Number of chains: 14 Chain: "I" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "J" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "M" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "N" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "O" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "P" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 591 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "R" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "X" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 367 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "Y" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 367 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "a" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2243 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.20 Number of scatterers: 8915 At special positions: 0 Unit cell: (92.13, 100.43, 97.11, 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) Zn 1 29.99 S 65 16.00 O 1497 8.00 N 1392 7.00 C 5960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 275.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 301 " pdb="ZN ZN a 301 " - pdb=" ND1 HIS a 186 " pdb="ZN ZN a 301 " - pdb=" ND1 HIS a 289 " 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 1 sheets defined 89.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'I' and resid 1 through 41 removed outlier: 3.531A pdb=" N ALA I 9 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE I 10 " --> pdb=" O GLY I 6 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 60 removed outlier: 3.729A pdb=" N GLY I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 76 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 2 through 41 removed outlier: 3.663A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 removed outlier: 3.578A pdb=" N LEU J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 removed outlier: 3.566A pdb=" N ILE J 65 " --> pdb=" O ALA J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'L' and resid 2 through 41 removed outlier: 3.530A pdb=" N ALA L 9 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE L 10 " --> pdb=" O GLY L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 76 removed outlier: 3.558A pdb=" N VAL L 50 " --> pdb=" O PRO L 46 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 58 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N THR L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE L 65 " --> pdb=" O ALA L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 82 removed outlier: 3.691A pdb=" N GLY L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 41 Processing helix chain 'M' and resid 44 through 76 removed outlier: 3.704A pdb=" N LEU M 58 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE M 65 " --> pdb=" O ALA M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.542A pdb=" N ILE M 83 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 41 removed outlier: 3.748A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 60 removed outlier: 3.789A pdb=" N LEU N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP N 60 " --> pdb=" O ALA N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 76 removed outlier: 3.653A pdb=" N PHE N 75 " --> pdb=" O LEU N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 4.014A pdb=" N GLY N 81 " --> pdb=" O ASN N 77 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN N 82 " --> pdb=" O PRO N 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 77 through 82' Processing helix chain 'O' and resid 2 through 41 removed outlier: 3.548A pdb=" N ALA O 9 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE O 10 " --> pdb=" O GLY O 6 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 75 removed outlier: 3.540A pdb=" N VAL O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU O 58 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 83 removed outlier: 4.537A pdb=" N GLY O 81 " --> pdb=" O ASN O 77 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN O 82 " --> pdb=" O PRO O 78 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE O 83 " --> pdb=" O PHE O 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 77 through 83' Processing helix chain 'P' and resid 2 through 41 removed outlier: 3.515A pdb=" N ILE P 10 " --> pdb=" O GLY P 6 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY P 19 " --> pdb=" O LEU P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 removed outlier: 3.529A pdb=" N VAL P 50 " --> pdb=" O PRO P 46 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU P 58 " --> pdb=" O ILE P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 76 Processing helix chain 'Q' and resid 2 through 41 Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.542A pdb=" N VAL Q 50 " --> pdb=" O PRO Q 46 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU Q 58 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 76 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'R' and resid 2 through 41 removed outlier: 3.660A pdb=" N GLY R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.798A pdb=" N VAL R 50 " --> pdb=" O PRO R 46 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 76 removed outlier: 3.553A pdb=" N ILE R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 41 removed outlier: 3.702A pdb=" N ILE S 10 " --> pdb=" O GLY S 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 76 removed outlier: 3.633A pdb=" N VAL S 50 " --> pdb=" O PRO S 46 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N THR S 63 " --> pdb=" O LEU S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'X' and resid 5 through 25 removed outlier: 3.632A pdb=" N GLY X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER X 11 " --> pdb=" O LEU X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 44 removed outlier: 3.599A pdb=" N VAL X 29 " --> pdb=" O VAL X 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 25 Processing helix chain 'Y' and resid 25 through 47 removed outlier: 3.630A pdb=" N VAL Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 14 removed outlier: 3.507A pdb=" N HIS a 13 " --> pdb=" O TYR a 9 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU a 14 " --> pdb=" O ILE a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 32 through 39 removed outlier: 3.642A pdb=" N MET a 39 " --> pdb=" O GLN a 35 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 66 removed outlier: 3.602A pdb=" N LEU a 54 " --> pdb=" O GLY a 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA a 66 " --> pdb=" O ILE a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 95 Processing helix chain 'a' and resid 103 through 121 removed outlier: 3.842A pdb=" N ILE a 121 " --> pdb=" O LEU a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 124 No H-bonds generated for 'chain 'a' and resid 122 through 124' Processing helix chain 'a' and resid 127 through 138 Processing helix chain 'a' and resid 147 through 150 removed outlier: 3.537A pdb=" N THR a 150 " --> pdb=" O VAL a 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 147 through 150' Processing helix chain 'a' and resid 151 through 185 removed outlier: 3.566A pdb=" N THR a 155 " --> pdb=" O ASP a 151 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER a 161 " --> pdb=" O GLY a 157 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL a 162 " --> pdb=" O LEU a 158 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE a 176 " --> pdb=" O LYS a 172 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N GLY a 177 " --> pdb=" O VAL a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 197 Processing helix chain 'a' and resid 199 through 242 removed outlier: 3.720A pdb=" N LYS a 214 " --> pdb=" O THR a 210 " (cutoff:3.500A) Proline residue: a 215 - end of helix removed outlier: 3.857A pdb=" N LEU a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL a 238 " --> pdb=" O ILE a 234 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET a 239 " --> pdb=" O LEU a 235 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE a 240 " --> pdb=" O ILE a 236 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER a 242 " --> pdb=" O VAL a 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 283 removed outlier: 3.945A pdb=" N LEU a 250 " --> pdb=" O LEU a 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL a 252 " --> pdb=" O SER a 248 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA a 253 " --> pdb=" O ALA a 249 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU a 264 " --> pdb=" O VAL a 260 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 18 through 20 809 hydrogen bonds defined for protein. 2400 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1738 1.33 - 1.45: 1922 1.45 - 1.57: 5295 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 9083 Sorted by residual: bond pdb=" N VAL N 62 " pdb=" CA VAL N 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.33e-02 5.65e+03 6.49e+00 bond pdb=" N ASP N 60 " pdb=" CA ASP N 60 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.22e-02 6.72e+03 5.19e+00 bond pdb=" N GLN R 82 " pdb=" CA GLN R 82 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.37e-02 5.33e+03 4.53e+00 bond pdb=" CA ALA N 61 " pdb=" CB ALA N 61 " ideal model delta sigma weight residual 1.530 1.498 0.032 1.57e-02 4.06e+03 4.13e+00 bond pdb=" C VAL N 62 " pdb=" O VAL N 62 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.32e-02 5.74e+03 3.29e+00 ... (remaining 9078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 12034 1.57 - 3.14: 213 3.14 - 4.71: 39 4.71 - 6.28: 21 6.28 - 7.85: 6 Bond angle restraints: 12313 Sorted by residual: angle pdb=" C ALA J 76 " pdb=" N ASN J 77 " pdb=" CA ASN J 77 " ideal model delta sigma weight residual 122.26 115.94 6.32 1.10e+00 8.26e-01 3.30e+01 angle pdb=" C ALA I 76 " pdb=" N ASN I 77 " pdb=" CA ASN I 77 " ideal model delta sigma weight residual 122.26 116.44 5.82 1.10e+00 8.26e-01 2.80e+01 angle pdb=" C ALA S 76 " pdb=" N ASN S 77 " pdb=" CA ASN S 77 " ideal model delta sigma weight residual 122.26 116.54 5.72 1.10e+00 8.26e-01 2.70e+01 angle pdb=" C MET O 44 " pdb=" N VAL O 45 " pdb=" CA VAL O 45 " ideal model delta sigma weight residual 120.24 123.38 -3.14 6.30e-01 2.52e+00 2.48e+01 angle pdb=" N THR N 63 " pdb=" CA THR N 63 " pdb=" C THR N 63 " ideal model delta sigma weight residual 112.23 106.92 5.31 1.26e+00 6.30e-01 1.78e+01 ... (remaining 12308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4913 17.81 - 35.63: 251 35.63 - 53.44: 46 53.44 - 71.25: 6 71.25 - 89.06: 5 Dihedral angle restraints: 5221 sinusoidal: 1911 harmonic: 3310 Sorted by residual: dihedral pdb=" CA PHE M 75 " pdb=" C PHE M 75 " pdb=" N ALA M 76 " pdb=" CA ALA M 76 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA PHE N 75 " pdb=" C PHE N 75 " pdb=" N ALA N 76 " pdb=" CA ALA N 76 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLY R 81 " pdb=" C GLY R 81 " pdb=" N GLN R 82 " pdb=" CA GLN R 82 " ideal model delta harmonic sigma weight residual -180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 5218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 986 0.034 - 0.068: 404 0.068 - 0.103: 105 0.103 - 0.137: 19 0.137 - 0.171: 4 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CA HIS a 186 " pdb=" N HIS a 186 " pdb=" C HIS a 186 " pdb=" CB HIS a 186 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CB THR N 63 " pdb=" CA THR N 63 " pdb=" OG1 THR N 63 " pdb=" CG2 THR N 63 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA LEU N 59 " pdb=" N LEU N 59 " pdb=" C LEU N 59 " pdb=" CB LEU N 59 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1515 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA a 284 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ALA a 284 " -0.062 2.00e-02 2.50e+03 pdb=" O ALA a 284 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS a 285 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 81 " 0.015 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C GLY R 81 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY R 81 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN R 82 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 56 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C ALA N 56 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA N 56 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY N 57 " 0.014 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 4 2.57 - 3.15: 7330 3.15 - 3.73: 14011 3.73 - 4.32: 18951 4.32 - 4.90: 32993 Nonbonded interactions: 73289 Sorted by model distance: nonbonded pdb=" OE2 GLU a 182 " pdb="ZN ZN a 301 " model vdw 1.984 2.230 nonbonded pdb=" OD1 ASP a 287 " pdb="ZN ZN a 301 " model vdw 1.995 2.230 nonbonded pdb=" O ASP N 60 " pdb=" OD1 ASP N 60 " model vdw 2.184 3.040 nonbonded pdb=" OE2 GLU a 182 " pdb=" OD1 ASP a 287 " model vdw 2.437 3.040 nonbonded pdb=" N ALA M 76 " pdb=" O ALA M 76 " model vdw 2.587 2.496 ... (remaining 73284 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 'I' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'J' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'L' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'M' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'N' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'O' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = chain 'P' selection = (chain 'Q' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'R' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'S' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.310 Find NCS groups from input model: 0.140 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:9.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.005 0.268 9085 Z= 0.223 Angle : 0.612 7.855 12313 Z= 0.370 Chirality : 0.039 0.171 1518 Planarity : 0.004 0.038 1522 Dihedral : 11.625 89.062 3113 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.33 % Allowed : 4.65 % Favored : 93.02 % 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: 1.89 (0.24), residues: 1184 helix: 1.75 (0.16), residues: 1021 sheet: None (None), residues: 0 loop : -1.88 (0.43), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 40 TYR 0.007 0.001 TYR a 227 PHE 0.011 0.001 PHE X 14 TRP 0.007 0.001 TRP a 42 HIS 0.004 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9083) covalent geometry : angle 0.61199 (12313) hydrogen bonds : bond 0.13283 ( 809) hydrogen bonds : angle 5.21957 ( 2400) metal coordination : bond 0.26626 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.320 Fit side-chains REVERT: M 64 MET cc_start: 0.8278 (mmt) cc_final: 0.8014 (mmt) outliers start: 21 outliers final: 6 residues processed: 203 average time/residue: 0.6912 time to fit residues: 147.7303 Evaluate side-chains 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain a residue 24 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN P 82 GLN R 82 GLN S 82 GLN X 4 ASN X 37 GLN a 45 HIS a 79 GLN a 285 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.078871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.058872 restraints weight = 15374.313| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.86 r_work: 0.2767 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9085 Z= 0.155 Angle : 0.582 10.128 12313 Z= 0.293 Chirality : 0.039 0.140 1518 Planarity : 0.004 0.040 1522 Dihedral : 4.672 57.751 1229 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.66 % Allowed : 13.51 % Favored : 83.83 % 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 (0.24), residues: 1184 helix: 2.07 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -2.01 (0.41), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Y 36 TYR 0.006 0.001 TYR a 227 PHE 0.013 0.001 PHE X 20 TRP 0.005 0.001 TRP a 42 HIS 0.003 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9083) covalent geometry : angle 0.58178 (12313) hydrogen bonds : bond 0.05880 ( 809) hydrogen bonds : angle 4.09781 ( 2400) metal coordination : bond 0.00531 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.348 Fit side-chains REVERT: I 44 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7978 (mtp) REVERT: I 60 ASP cc_start: 0.7372 (p0) cc_final: 0.7068 (p0) REVERT: N 44 MET cc_start: 0.8063 (mtm) cc_final: 0.7620 (mtp) REVERT: a 206 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7575 (tt) REVERT: a 207 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8062 (mm-30) outliers start: 24 outliers final: 11 residues processed: 153 average time/residue: 0.7222 time to fit residues: 116.3525 Evaluate side-chains 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain X residue 38 LYS Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 206 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN N 41 GLN X 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.081279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.061214 restraints weight = 15232.825| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.86 r_work: 0.2822 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9085 Z= 0.125 Angle : 0.507 7.505 12313 Z= 0.261 Chirality : 0.037 0.145 1518 Planarity : 0.004 0.038 1522 Dihedral : 4.415 58.677 1227 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.88 % Allowed : 14.62 % Favored : 82.50 % 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: 2.77 (0.24), residues: 1184 helix: 2.38 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -1.96 (0.40), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 40 TYR 0.004 0.001 TYR a 227 PHE 0.011 0.001 PHE X 14 TRP 0.005 0.001 TRP a 42 HIS 0.002 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9083) covalent geometry : angle 0.50662 (12313) hydrogen bonds : bond 0.04896 ( 809) hydrogen bonds : angle 3.82953 ( 2400) metal coordination : bond 0.00444 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.359 Fit side-chains REVERT: I 44 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7696 (mtp) REVERT: I 60 ASP cc_start: 0.7240 (p0) cc_final: 0.6933 (p0) REVERT: N 1 MET cc_start: 0.7407 (ttm) cc_final: 0.7187 (tpt) REVERT: N 44 MET cc_start: 0.7956 (mtm) cc_final: 0.7566 (mtp) REVERT: O 44 MET cc_start: 0.7643 (mmt) cc_final: 0.7437 (mmp) REVERT: Q 2 GLU cc_start: 0.8279 (mp0) cc_final: 0.7490 (mt-10) REVERT: R 40 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7442 (ttm-80) REVERT: a 172 LYS cc_start: 0.7364 (tppt) cc_final: 0.6909 (tttm) REVERT: a 206 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7474 (tt) outliers start: 26 outliers final: 6 residues processed: 146 average time/residue: 0.7740 time to fit residues: 118.6848 Evaluate side-chains 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain a residue 206 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 41 GLN O 49 GLN X 4 ASN X 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.079899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.060180 restraints weight = 15395.476| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.83 r_work: 0.2802 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9085 Z= 0.141 Angle : 0.540 9.746 12313 Z= 0.273 Chirality : 0.038 0.150 1518 Planarity : 0.004 0.039 1522 Dihedral : 3.971 41.517 1223 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.43 % Allowed : 14.62 % Favored : 81.95 % 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: 2.84 (0.24), residues: 1184 helix: 2.42 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -1.91 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 40 TYR 0.004 0.001 TYR a 169 PHE 0.013 0.001 PHE N 72 TRP 0.005 0.001 TRP a 42 HIS 0.002 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9083) covalent geometry : angle 0.53989 (12313) hydrogen bonds : bond 0.05236 ( 809) hydrogen bonds : angle 3.79935 ( 2400) metal coordination : bond 0.00117 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.355 Fit side-chains REVERT: I 44 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7766 (mtp) REVERT: I 60 ASP cc_start: 0.7360 (p0) cc_final: 0.7054 (p0) REVERT: J 1 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6830 (tpp) REVERT: J 2 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: N 44 MET cc_start: 0.7897 (mtm) cc_final: 0.7338 (ptp) REVERT: O 43 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8059 (pm20) REVERT: O 44 MET cc_start: 0.7754 (mmt) cc_final: 0.7507 (mmp) REVERT: R 40 ARG cc_start: 0.7960 (ttm170) cc_final: 0.7455 (ttm110) REVERT: a 172 LYS cc_start: 0.7454 (tppt) cc_final: 0.7023 (tttm) REVERT: a 206 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7514 (tt) REVERT: a 207 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8002 (mm-30) outliers start: 31 outliers final: 15 residues processed: 150 average time/residue: 0.7569 time to fit residues: 119.4098 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 49 GLN Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain X residue 38 LYS Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 107 optimal weight: 0.0000 chunk 101 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 62 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 overall best weight: 1.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 41 GLN O 49 GLN X 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.079421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.059929 restraints weight = 15497.646| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.82 r_work: 0.2799 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9085 Z= 0.139 Angle : 0.525 6.648 12313 Z= 0.270 Chirality : 0.038 0.145 1518 Planarity : 0.004 0.039 1522 Dihedral : 3.963 39.916 1223 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.32 % Allowed : 15.61 % Favored : 81.06 % 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: 2.91 (0.24), residues: 1184 helix: 2.46 (0.15), residues: 1024 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 40 TYR 0.005 0.001 TYR a 169 PHE 0.012 0.001 PHE N 72 TRP 0.005 0.001 TRP a 42 HIS 0.002 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9083) covalent geometry : angle 0.52485 (12313) hydrogen bonds : bond 0.05209 ( 809) hydrogen bonds : angle 3.77092 ( 2400) metal coordination : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.245 Fit side-chains REVERT: I 44 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7736 (mtt) REVERT: I 60 ASP cc_start: 0.7345 (p0) cc_final: 0.7044 (p0) REVERT: J 2 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: N 44 MET cc_start: 0.7924 (mtm) cc_final: 0.7338 (ptp) REVERT: O 43 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8046 (pm20) REVERT: O 44 MET cc_start: 0.7768 (mmt) cc_final: 0.7514 (mmp) REVERT: P 1 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7391 (ttm) REVERT: Q 2 GLU cc_start: 0.8250 (mp0) cc_final: 0.7468 (mt-10) REVERT: R 40 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7425 (ttm110) REVERT: a 172 LYS cc_start: 0.7458 (tppt) cc_final: 0.7027 (tttm) REVERT: a 206 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7526 (tt) REVERT: a 207 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7994 (mm-30) outliers start: 30 outliers final: 14 residues processed: 145 average time/residue: 0.7623 time to fit residues: 116.3209 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain X residue 45 ASP Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.059997 restraints weight = 15414.579| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.85 r_work: 0.2794 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9085 Z= 0.134 Angle : 0.520 7.128 12313 Z= 0.266 Chirality : 0.038 0.146 1518 Planarity : 0.004 0.039 1522 Dihedral : 3.920 39.499 1223 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.43 % Allowed : 16.17 % Favored : 80.40 % 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: 3.02 (0.24), residues: 1184 helix: 2.53 (0.15), residues: 1024 sheet: None (None), residues: 0 loop : -1.80 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 40 TYR 0.005 0.001 TYR a 169 PHE 0.012 0.001 PHE X 14 TRP 0.005 0.001 TRP a 42 HIS 0.002 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9083) covalent geometry : angle 0.51964 (12313) hydrogen bonds : bond 0.05097 ( 809) hydrogen bonds : angle 3.73510 ( 2400) metal coordination : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.381 Fit side-chains REVERT: I 44 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7719 (mtt) REVERT: I 60 ASP cc_start: 0.7359 (p0) cc_final: 0.7041 (p0) REVERT: J 2 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: N 44 MET cc_start: 0.7982 (mtm) cc_final: 0.7305 (ptp) REVERT: O 43 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7994 (pm20) REVERT: O 44 MET cc_start: 0.7741 (mmt) cc_final: 0.7491 (mmp) REVERT: P 1 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7383 (ttm) REVERT: Q 2 GLU cc_start: 0.8236 (mp0) cc_final: 0.7421 (mt-10) REVERT: R 40 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7430 (ttm110) REVERT: a 172 LYS cc_start: 0.7434 (tppt) cc_final: 0.6993 (tttm) REVERT: a 206 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7488 (tt) outliers start: 31 outliers final: 16 residues processed: 147 average time/residue: 0.7359 time to fit residues: 113.9180 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain X residue 45 ASP Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.0070 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 41 GLN X 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.081337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.061350 restraints weight = 15459.609| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.84 r_work: 0.2822 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9085 Z= 0.121 Angle : 0.502 10.239 12313 Z= 0.257 Chirality : 0.037 0.129 1518 Planarity : 0.004 0.038 1522 Dihedral : 3.838 39.453 1223 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.21 % Allowed : 16.06 % Favored : 80.73 % 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: 3.20 (0.24), residues: 1184 helix: 2.65 (0.15), residues: 1024 sheet: None (None), residues: 0 loop : -1.72 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 40 TYR 0.003 0.001 TYR a 169 PHE 0.012 0.001 PHE X 14 TRP 0.005 0.001 TRP a 42 HIS 0.001 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9083) covalent geometry : angle 0.50223 (12313) hydrogen bonds : bond 0.04709 ( 809) hydrogen bonds : angle 3.68130 ( 2400) metal coordination : bond 0.00058 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: I 44 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7630 (mtt) REVERT: I 60 ASP cc_start: 0.7282 (p0) cc_final: 0.6944 (p0) REVERT: J 2 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7109 (tt0) REVERT: N 44 MET cc_start: 0.7781 (mtm) cc_final: 0.7492 (ptp) REVERT: O 43 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7975 (pm20) REVERT: O 44 MET cc_start: 0.7699 (mmt) cc_final: 0.7443 (mmp) REVERT: P 1 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7319 (ttm) REVERT: Q 2 GLU cc_start: 0.8192 (mp0) cc_final: 0.7403 (mt-10) REVERT: R 2 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: a 172 LYS cc_start: 0.7425 (tppt) cc_final: 0.6971 (tttm) REVERT: a 207 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8025 (mm-30) outliers start: 29 outliers final: 15 residues processed: 149 average time/residue: 0.7402 time to fit residues: 116.1642 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 64 MET Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 49 GLN X 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.057973 restraints weight = 15436.345| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.82 r_work: 0.2747 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9085 Z= 0.177 Angle : 0.581 7.558 12313 Z= 0.292 Chirality : 0.039 0.157 1518 Planarity : 0.004 0.039 1522 Dihedral : 4.015 38.252 1223 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.21 % Allowed : 16.28 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.23), residues: 1184 helix: 2.48 (0.15), residues: 1025 sheet: None (None), residues: 0 loop : -1.78 (0.42), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 40 TYR 0.005 0.001 TYR a 169 PHE 0.016 0.002 PHE N 72 TRP 0.004 0.001 TRP Y 26 HIS 0.002 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9083) covalent geometry : angle 0.58102 (12313) hydrogen bonds : bond 0.05857 ( 809) hydrogen bonds : angle 3.79802 ( 2400) metal coordination : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: I 44 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7691 (mtt) REVERT: I 60 ASP cc_start: 0.7456 (p0) cc_final: 0.7110 (p0) REVERT: N 44 MET cc_start: 0.7904 (mtm) cc_final: 0.7564 (ptp) REVERT: O 43 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8017 (pm20) REVERT: O 44 MET cc_start: 0.7781 (mmt) cc_final: 0.7522 (mmp) REVERT: P 1 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7442 (ttm) REVERT: Q 2 GLU cc_start: 0.8304 (mp0) cc_final: 0.7553 (mt-10) REVERT: R 2 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: a 172 LYS cc_start: 0.7474 (tppt) cc_final: 0.7082 (tmmt) REVERT: a 207 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7990 (mm-30) outliers start: 29 outliers final: 14 residues processed: 145 average time/residue: 0.7656 time to fit residues: 116.6829 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 49 GLN Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain X residue 45 ASP Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 283 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 41 GLN O 49 GLN X 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.080630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.060677 restraints weight = 15652.815| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.85 r_work: 0.2809 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9085 Z= 0.123 Angle : 0.510 10.723 12313 Z= 0.262 Chirality : 0.037 0.126 1518 Planarity : 0.004 0.038 1522 Dihedral : 3.707 21.991 1220 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.77 % Allowed : 17.83 % Favored : 80.40 % 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: 3.23 (0.24), residues: 1184 helix: 2.65 (0.15), residues: 1025 sheet: None (None), residues: 0 loop : -1.60 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 40 TYR 0.002 0.000 TYR a 9 PHE 0.012 0.001 PHE X 14 TRP 0.006 0.001 TRP a 42 HIS 0.001 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9083) covalent geometry : angle 0.51034 (12313) hydrogen bonds : bond 0.04823 ( 809) hydrogen bonds : angle 3.70921 ( 2400) metal coordination : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.369 Fit side-chains REVERT: I 44 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7639 (mtt) REVERT: I 60 ASP cc_start: 0.7362 (p0) cc_final: 0.7033 (p0) REVERT: N 44 MET cc_start: 0.7796 (mtm) cc_final: 0.7390 (ptp) REVERT: O 43 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7966 (pm20) REVERT: O 44 MET cc_start: 0.7708 (mmt) cc_final: 0.7458 (mmp) REVERT: P 1 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7452 (ttm) REVERT: Q 2 GLU cc_start: 0.8169 (mp0) cc_final: 0.7426 (mt-10) REVERT: R 2 GLU cc_start: 0.7838 (pm20) cc_final: 0.7584 (pm20) REVERT: a 172 LYS cc_start: 0.7439 (tppt) cc_final: 0.7055 (tmmt) REVERT: a 207 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8038 (mm-30) outliers start: 16 outliers final: 11 residues processed: 144 average time/residue: 0.7766 time to fit residues: 117.4836 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.6980 chunk 7 optimal weight: 0.0170 chunk 77 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 41 GLN a 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.062214 restraints weight = 15519.222| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.86 r_work: 0.2843 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9085 Z= 0.118 Angle : 0.501 7.358 12313 Z= 0.256 Chirality : 0.036 0.130 1518 Planarity : 0.004 0.038 1522 Dihedral : 3.541 18.193 1220 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.55 % Allowed : 18.38 % Favored : 80.07 % 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: 3.45 (0.23), residues: 1184 helix: 2.81 (0.15), residues: 1024 sheet: None (None), residues: 0 loop : -1.55 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 40 TYR 0.003 0.000 TYR a 227 PHE 0.012 0.001 PHE X 14 TRP 0.005 0.001 TRP a 51 HIS 0.001 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9083) covalent geometry : angle 0.50129 (12313) hydrogen bonds : bond 0.04518 ( 809) hydrogen bonds : angle 3.62655 ( 2400) metal coordination : bond 0.00048 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.366 Fit side-chains REVERT: I 44 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7646 (mtt) REVERT: I 60 ASP cc_start: 0.7327 (p0) cc_final: 0.7000 (p0) REVERT: N 44 MET cc_start: 0.7615 (mtm) cc_final: 0.7411 (ptp) REVERT: O 44 MET cc_start: 0.7673 (mmt) cc_final: 0.7456 (mmp) REVERT: P 1 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7325 (ttm) REVERT: Q 2 GLU cc_start: 0.8094 (mp0) cc_final: 0.7312 (mt-10) REVERT: R 44 MET cc_start: 0.8164 (mmp) cc_final: 0.7961 (mmm) REVERT: a 172 LYS cc_start: 0.7439 (tppt) cc_final: 0.6975 (tttm) REVERT: a 207 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7501 (mp0) outliers start: 14 outliers final: 9 residues processed: 141 average time/residue: 0.7547 time to fit residues: 111.8988 Evaluate side-chains 139 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 chunk 7 optimal weight: 0.0170 chunk 70 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 49 GLN X 4 ASN X 37 GLN Y 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.083584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.063858 restraints weight = 15484.729| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.85 r_work: 0.2884 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9085 Z= 0.113 Angle : 0.489 8.533 12313 Z= 0.250 Chirality : 0.036 0.126 1518 Planarity : 0.004 0.038 1522 Dihedral : 3.461 15.083 1220 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.44 % Allowed : 18.72 % Favored : 79.84 % 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: 3.64 (0.23), residues: 1184 helix: 2.92 (0.15), residues: 1024 sheet: None (None), residues: 0 loop : -1.41 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 40 TYR 0.003 0.000 TYR a 9 PHE 0.013 0.001 PHE X 14 TRP 0.005 0.001 TRP a 42 HIS 0.001 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 9083) covalent geometry : angle 0.48917 (12313) hydrogen bonds : bond 0.04192 ( 809) hydrogen bonds : angle 3.55261 ( 2400) metal coordination : bond 0.00027 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3499.18 seconds wall clock time: 60 minutes 28.12 seconds (3628.12 seconds total)