Starting phenix.real_space_refine on Thu Jul 2 22:09:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m30_23640/07_2026/7m30_23640.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m30_23640/07_2026/7m30_23640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m30_23640/07_2026/7m30_23640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m30_23640/07_2026/7m30_23640.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m30_23640/07_2026/7m30_23640.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m30_23640/07_2026/7m30_23640.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m30_23640/07_2026/7m30_23640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m30_23640/07_2026/7m30_23640.map" } resolution = 3.81 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1676 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5777 2.51 5 N 1591 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9191 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 78} Chain: "C" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1090 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "D" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1384 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 158} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 893 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain breaks: 1 Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "M" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 775 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 94} Chain breaks: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.56, per 1000 atoms: 0.17 Number of scatterers: 9191 At special positions: 0 Unit cell: (83.85, 142.975, 145.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1776 8.00 N 1591 7.00 C 5777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 49 " distance=2.03 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 207 " distance=2.02 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 40 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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 Links applied NAG-ASN " NAG D 300 " - " ASN D 201 " " NAG E 200 " - " ASN E 81 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 318.8 milliseconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 22 sheets defined 20.7% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.715A pdb=" N LEU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 132 through 142 removed outlier: 3.816A pdb=" N GLY B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.668A pdb=" N GLY C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 5.394A pdb=" N HIS C 82 " --> pdb=" O THR C 79 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 83 " --> pdb=" O MET C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 92 through 97 removed outlier: 5.667A pdb=" N SER C 95 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.837A pdb=" N ARG D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.995A pdb=" N LYS D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL D 110 " --> pdb=" O TRP D 106 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 131 Proline residue: D 126 - end of helix removed outlier: 3.811A pdb=" N ALA D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 21 through 27 Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 45 through 69 Processing helix chain 'E' and resid 73 through 79 removed outlier: 4.022A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.794A pdb=" N VAL E 85 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.730A pdb=" N ALA F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.570A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.689A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.600A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 151 through 154 Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 50 removed outlier: 3.596A pdb=" N LYS C 47 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS C 49 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR C 53 " --> pdb=" O CYS C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 132 removed outlier: 3.847A pdb=" N GLU D 177 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG E 118 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 71 through 78 removed outlier: 6.669A pdb=" N TYR D 92 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE D 74 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU D 90 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN D 76 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU D 88 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.014A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.014A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.567A pdb=" N VAL G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.567A pdb=" N VAL G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.657A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.297A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.390A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER M 50 " --> pdb=" O TRP M 35A" (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP M 35A" --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.390A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER M 50 " --> pdb=" O TRP M 35A" (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP M 35A" --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.627A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 10 through 13 396 hydrogen bonds defined for protein. 984 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: 1.43 Time building geometry restraints manager: 1.07 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: 2990 1.34 - 1.47: 2486 1.47 - 1.60: 3862 1.60 - 1.73: 0 1.73 - 1.86: 64 Bond restraints: 9402 Sorted by residual: bond pdb=" CA VAL B 155 " pdb=" C VAL B 155 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.27e-02 6.20e+03 1.02e+01 bond pdb=" C LEU L 94 " pdb=" O LEU L 94 " ideal model delta sigma weight residual 1.239 1.219 0.020 9.60e-03 1.09e+04 4.14e+00 bond pdb=" CA GLN N 89 " pdb=" C GLN N 89 " ideal model delta sigma weight residual 1.520 1.498 0.022 1.16e-02 7.43e+03 3.67e+00 bond pdb=" CG GLU D 101 " pdb=" CD GLU D 101 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CA ASN N 96 " pdb=" C ASN N 96 " ideal model delta sigma weight residual 1.524 1.500 0.023 1.29e-02 6.01e+03 3.27e+00 ... (remaining 9397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 12308 2.72 - 5.43: 390 5.43 - 8.15: 46 8.15 - 10.86: 9 10.86 - 13.58: 9 Bond angle restraints: 12762 Sorted by residual: angle pdb=" N ASN N 97 " pdb=" CA ASN N 97 " pdb=" C ASN N 97 " ideal model delta sigma weight residual 110.53 120.78 -10.25 1.32e+00 5.74e-01 6.03e+01 angle pdb=" N CYS B 154 " pdb=" CA CYS B 154 " pdb=" C CYS B 154 " ideal model delta sigma weight residual 108.99 119.31 -10.32 1.57e+00 4.06e-01 4.32e+01 angle pdb=" CA SER F 97 " pdb=" C SER F 97 " pdb=" N THR F 98 " ideal model delta sigma weight residual 119.63 114.61 5.02 8.10e-01 1.52e+00 3.85e+01 angle pdb=" N ASP B 157 " pdb=" CA ASP B 157 " pdb=" C ASP B 157 " ideal model delta sigma weight residual 111.36 117.75 -6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" C ALA B 131 " pdb=" N PRO B 132 " pdb=" CA PRO B 132 " ideal model delta sigma weight residual 127.00 139.54 -12.54 2.40e+00 1.74e-01 2.73e+01 ... (remaining 12757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5101 17.43 - 34.85: 378 34.85 - 52.27: 95 52.27 - 69.70: 21 69.70 - 87.12: 11 Dihedral angle restraints: 5606 sinusoidal: 2221 harmonic: 3385 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 48.95 44.05 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 111 " pdb=" CB CYS C 111 " ideal model delta sinusoidal sigma weight residual -86.00 -45.01 -40.99 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual 93.00 53.60 39.40 1 1.00e+01 1.00e-02 2.18e+01 ... (remaining 5603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1005 0.064 - 0.128: 308 0.128 - 0.192: 67 0.192 - 0.256: 15 0.256 - 0.320: 4 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CG LEU M 69 " pdb=" CB LEU M 69 " pdb=" CD1 LEU M 69 " pdb=" CD2 LEU M 69 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ASN N 97 " pdb=" N ASN N 97 " pdb=" C ASN N 97 " pdb=" CB ASN N 97 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE G 75 " pdb=" CA ILE G 75 " pdb=" CG1 ILE G 75 " pdb=" CG2 ILE G 75 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 1396 not shown) Planarity restraints: 1645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 71 " -0.089 9.50e-02 1.11e+02 5.27e-02 1.58e+01 pdb=" NE ARG H 71 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG H 71 " -0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG H 71 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG H 71 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 86 " 0.092 9.50e-02 1.11e+02 5.32e-02 1.53e+01 pdb=" NE ARG C 86 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG C 86 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG C 86 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG C 86 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 22 " -0.081 9.50e-02 1.11e+02 4.79e-02 1.29e+01 pdb=" NE ARG E 22 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 22 " -0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG E 22 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG E 22 " 0.017 2.00e-02 2.50e+03 ... (remaining 1642 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 19 2.35 - 2.99: 4874 2.99 - 3.62: 13982 3.62 - 4.26: 21094 4.26 - 4.90: 34664 Nonbonded interactions: 74633 Sorted by model distance: nonbonded pdb=" OD1 ASP F 95 " pdb=" O TYR F 100D" model vdw 1.711 3.040 nonbonded pdb=" OD1 ASP B 103 " pdb=" N ALA B 104 " model vdw 2.218 3.120 nonbonded pdb=" NZ LYS C 117 " pdb=" O ASP G 29 " model vdw 2.236 3.120 nonbonded pdb=" OG SER N 7 " pdb=" OG1 THR N 22 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLN F 3 " pdb=" OG SER F 25 " model vdw 2.246 3.040 ... (remaining 74628 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 7.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 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 0.054 9419 Z= 0.262 Angle : 1.163 13.694 12798 Z= 0.644 Chirality : 0.067 0.320 1399 Planarity : 0.008 0.084 1643 Dihedral : 13.609 87.119 3397 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.89 % Allowed : 5.74 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.25), residues: 1141 helix: -1.66 (0.36), residues: 157 sheet: -0.07 (0.25), residues: 399 loop : -0.61 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.010 ARG H 71 TYR 0.028 0.005 TYR E 65 PHE 0.031 0.003 PHE D 190 TRP 0.035 0.003 TRP D 112 HIS 0.012 0.002 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.26 ( 9402) covalent geometry : angle 1.15137 / 0.64 (12762) SS BOND : bond 0.00843 / 0.41 ( 15) SS BOND : angle 3.30662 / 1.51 ( 30) hydrogen bonds : bond 0.13648 / 9.64 ( 368) hydrogen bonds : angle 7.46840 / 5.16 ( 984) link_NAG-ASN : bond 0.00327 / 0.16 ( 2) link_NAG-ASN : angle 3.30815 / 1.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 545 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7603 (mpt180) REVERT: B 114 ASN cc_start: 0.8619 (m-40) cc_final: 0.8417 (m110) REVERT: B 118 GLN cc_start: 0.8721 (pm20) cc_final: 0.8331 (pm20) REVERT: B 133 ARG cc_start: 0.8778 (ttp-170) cc_final: 0.8383 (ttt-90) REVERT: B 135 MET cc_start: 0.8752 (tmm) cc_final: 0.8317 (tmm) REVERT: C 46 PHE cc_start: 0.8842 (p90) cc_final: 0.8538 (p90) REVERT: C 72 GLU cc_start: 0.8464 (tp30) cc_final: 0.7793 (tp30) REVERT: C 76 ILE cc_start: 0.9034 (mt) cc_final: 0.8814 (mm) REVERT: C 85 THR cc_start: 0.8458 (t) cc_final: 0.8041 (m) REVERT: C 87 GLN cc_start: 0.8610 (pm20) cc_final: 0.8410 (tp40) REVERT: C 91 ASN cc_start: 0.8892 (m-40) cc_final: 0.8618 (m-40) REVERT: C 92 LYS cc_start: 0.9191 (mttm) cc_final: 0.8981 (mttp) REVERT: C 93 LEU cc_start: 0.8930 (mp) cc_final: 0.8443 (mp) REVERT: C 97 ASN cc_start: 0.8112 (m-40) cc_final: 0.7694 (m-40) REVERT: C 101 LEU cc_start: 0.8994 (mt) cc_final: 0.8669 (mt) REVERT: C 103 LEU cc_start: 0.8499 (tp) cc_final: 0.8232 (tp) REVERT: C 147 ASP cc_start: 0.8901 (m-30) cc_final: 0.8342 (m-30) REVERT: C 151 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8523 (mm-30) REVERT: D 94 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.8234 (mtt90) REVERT: D 95 GLU cc_start: 0.8807 (tp30) cc_final: 0.8521 (mt-10) REVERT: D 99 LEU cc_start: 0.7870 (tt) cc_final: 0.7421 (pp) REVERT: D 119 GLN cc_start: 0.8467 (pt0) cc_final: 0.8111 (pt0) REVERT: D 130 SER cc_start: 0.7493 (t) cc_final: 0.6832 (t) REVERT: D 142 GLU cc_start: 0.9168 (mp0) cc_final: 0.8941 (mp0) REVERT: D 143 ASP cc_start: 0.8976 (m-30) cc_final: 0.8701 (m-30) REVERT: D 159 LEU cc_start: 0.8750 (tp) cc_final: 0.8355 (tp) REVERT: D 160 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7578 (mpp80) REVERT: D 161 PHE cc_start: 0.8413 (p90) cc_final: 0.7610 (p90) REVERT: D 163 VAL cc_start: 0.8582 (t) cc_final: 0.8257 (p) REVERT: D 165 ASP cc_start: 0.7672 (p0) cc_final: 0.7189 (p0) REVERT: D 171 MET cc_start: 0.7626 (mmm) cc_final: 0.7364 (mmm) REVERT: D 174 MET cc_start: 0.8301 (ttp) cc_final: 0.8066 (ttp) REVERT: D 191 GLN cc_start: 0.7826 (pt0) cc_final: 0.7570 (pt0) REVERT: D 212 LEU cc_start: 0.9012 (mm) cc_final: 0.8582 (mp) REVERT: E 23 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8515 (mm-30) REVERT: E 29 ASP cc_start: 0.8633 (p0) cc_final: 0.8413 (p0) REVERT: E 30 TYR cc_start: 0.8697 (m-80) cc_final: 0.8333 (m-80) REVERT: E 44 LEU cc_start: 0.9063 (mp) cc_final: 0.8799 (mp) REVERT: E 51 LYS cc_start: 0.9188 (tttt) cc_final: 0.8979 (tttm) REVERT: E 54 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7676 (mm-30) REVERT: E 63 TYR cc_start: 0.8742 (t80) cc_final: 0.8438 (t80) REVERT: E 71 LEU cc_start: 0.8819 (mm) cc_final: 0.8585 (mt) REVERT: E 72 ASP cc_start: 0.8647 (p0) cc_final: 0.8370 (p0) REVERT: E 73 ASN cc_start: 0.7776 (t0) cc_final: 0.7522 (t0) REVERT: E 74 PHE cc_start: 0.8368 (t80) cc_final: 0.8120 (t80) REVERT: E 78 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8523 (ttmt) REVERT: E 88 LEU cc_start: 0.9044 (tt) cc_final: 0.8708 (tt) REVERT: E 92 PHE cc_start: 0.9098 (m-80) cc_final: 0.8864 (m-80) REVERT: E 121 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7489 (tm-30) REVERT: E 122 PHE cc_start: 0.8290 (p90) cc_final: 0.7791 (p90) REVERT: E 125 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.6766 (ttt-90) REVERT: F 57 THR cc_start: 0.7418 (p) cc_final: 0.7158 (p) REVERT: F 68 THR cc_start: 0.8194 (p) cc_final: 0.7921 (p) REVERT: F 69 ILE cc_start: 0.8595 (mt) cc_final: 0.8221 (mt) REVERT: F 97 SER cc_start: 0.8272 (p) cc_final: 0.7300 (p) REVERT: G 54 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.6784 (mtm110) REVERT: H 59 TYR cc_start: 0.5854 (m-80) cc_final: 0.5342 (m-80) REVERT: M 52 TYR cc_start: 0.5701 (t80) cc_final: 0.5401 (t80) REVERT: M 54 THR cc_start: 0.7213 (p) cc_final: 0.6971 (p) REVERT: M 58 PHE cc_start: 0.7560 (m-80) cc_final: 0.7247 (m-10) REVERT: M 63 PHE cc_start: 0.6046 (m-80) cc_final: 0.5632 (m-80) REVERT: M 67 VAL cc_start: 0.7199 (m) cc_final: 0.6980 (p) REVERT: M 69 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6734 (tp) REVERT: N 106 ILE cc_start: 0.3932 (pt) cc_final: 0.3441 (pt) outliers start: 9 outliers final: 4 residues processed: 550 average time/residue: 0.0946 time to fit residues: 67.7284 Evaluate side-chains 470 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 465 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain M residue 69 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 90 HIS C 99 ASN D 76 GLN E 129 ASN F 64 GLN G 37 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS L 79 GLN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.102105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.087552 restraints weight = 29924.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.090617 restraints weight = 16982.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.092716 restraints weight = 11055.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.094185 restraints weight = 7847.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.095269 restraints weight = 5928.067| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 9419 Z= 0.210 Angle : 0.874 12.957 12798 Z= 0.450 Chirality : 0.052 0.214 1399 Planarity : 0.006 0.060 1643 Dihedral : 6.327 46.646 1299 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.35 % Allowed : 19.78 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.25), residues: 1141 helix: -0.90 (0.38), residues: 156 sheet: 0.12 (0.25), residues: 406 loop : -0.24 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 38 TYR 0.027 0.003 TYR D 56 PHE 0.029 0.003 PHE D 147 TRP 0.028 0.003 TRP F 47 HIS 0.012 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 ( 9402) covalent geometry : angle 0.86814 / 0.45 (12762) SS BOND : bond 0.00638 / 0.35 ( 15) SS BOND : angle 1.93035 / 1.15 ( 30) hydrogen bonds : bond 0.04920 / 3.33 ( 368) hydrogen bonds : angle 6.48459 / 4.56 ( 984) link_NAG-ASN : bond 0.00037 / 0.02 ( 2) link_NAG-ASN : angle 2.65909 / 1.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 501 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ARG cc_start: 0.7789 (mpt180) cc_final: 0.7551 (mpt180) REVERT: B 99 VAL cc_start: 0.8634 (p) cc_final: 0.8229 (t) REVERT: B 118 GLN cc_start: 0.8582 (pm20) cc_final: 0.8194 (pm20) REVERT: B 133 ARG cc_start: 0.8684 (ttp-170) cc_final: 0.8417 (ttt180) REVERT: B 135 MET cc_start: 0.8244 (tmm) cc_final: 0.7954 (tmm) REVERT: B 136 THR cc_start: 0.8750 (m) cc_final: 0.8524 (p) REVERT: B 162 TYR cc_start: 0.6889 (m-80) cc_final: 0.6650 (m-80) REVERT: C 32 GLU cc_start: 0.2963 (OUTLIER) cc_final: 0.2378 (mp0) REVERT: C 44 TYR cc_start: 0.7992 (p90) cc_final: 0.7522 (p90) REVERT: C 48 MET cc_start: 0.8451 (mpp) cc_final: 0.8224 (mmp) REVERT: C 72 GLU cc_start: 0.8247 (tp30) cc_final: 0.7569 (tp30) REVERT: C 74 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8049 (ttp80) REVERT: C 76 ILE cc_start: 0.9180 (mt) cc_final: 0.8944 (mm) REVERT: C 85 THR cc_start: 0.8446 (t) cc_final: 0.7727 (m) REVERT: C 91 ASN cc_start: 0.8904 (m-40) cc_final: 0.8616 (m-40) REVERT: C 92 LYS cc_start: 0.9131 (mttm) cc_final: 0.8917 (mttp) REVERT: C 97 ASN cc_start: 0.8194 (m-40) cc_final: 0.7920 (m-40) REVERT: C 104 GLU cc_start: 0.8141 (tt0) cc_final: 0.7757 (tt0) REVERT: C 147 ASP cc_start: 0.8551 (m-30) cc_final: 0.8116 (m-30) REVERT: D 99 LEU cc_start: 0.8294 (tt) cc_final: 0.7849 (pp) REVERT: D 119 GLN cc_start: 0.8419 (pt0) cc_final: 0.8182 (pt0) REVERT: D 136 ASN cc_start: 0.8026 (p0) cc_final: 0.7788 (p0) REVERT: D 143 ASP cc_start: 0.8721 (m-30) cc_final: 0.8514 (m-30) REVERT: D 151 MET cc_start: 0.7683 (mtm) cc_final: 0.7411 (mtm) REVERT: D 160 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7635 (mtm110) REVERT: D 191 GLN cc_start: 0.7913 (pt0) cc_final: 0.7637 (pt0) REVERT: D 193 ARG cc_start: 0.8449 (ptp-110) cc_final: 0.8238 (ptp-110) REVERT: D 212 LEU cc_start: 0.8887 (mm) cc_final: 0.8544 (mp) REVERT: E 23 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8315 (mm-30) REVERT: E 51 LYS cc_start: 0.9126 (tttt) cc_final: 0.8913 (tttm) REVERT: E 54 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7300 (mm-30) REVERT: E 71 LEU cc_start: 0.8873 (mm) cc_final: 0.8662 (mt) REVERT: E 73 ASN cc_start: 0.8014 (t0) cc_final: 0.7800 (t0) REVERT: E 121 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7503 (tm-30) REVERT: E 122 PHE cc_start: 0.8311 (p90) cc_final: 0.7932 (p90) REVERT: E 125 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.6521 (ttt-90) REVERT: F 37 VAL cc_start: 0.8313 (t) cc_final: 0.7849 (m) REVERT: F 66 ARG cc_start: 0.8311 (mtm110) cc_final: 0.8008 (mtp180) REVERT: F 82 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8416 (tt) REVERT: F 91 PHE cc_start: 0.7475 (m-10) cc_final: 0.7228 (m-10) REVERT: F 100 TYR cc_start: 0.7168 (t80) cc_final: 0.6800 (t80) REVERT: G 27 ARG cc_start: 0.8450 (ptt-90) cc_final: 0.8001 (ptt-90) REVERT: G 31 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8063 (mtmm) REVERT: G 37 GLN cc_start: 0.7642 (tt0) cc_final: 0.7406 (tt0) REVERT: G 54 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7287 (mtp-110) REVERT: G 60 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7868 (mt-10) REVERT: G 105 THR cc_start: 0.5448 (p) cc_final: 0.4801 (p) REVERT: H 27 PHE cc_start: 0.7851 (p90) cc_final: 0.7413 (p90) REVERT: H 36 TRP cc_start: 0.6899 (m100) cc_final: 0.6067 (m100) REVERT: H 57 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8153 (mttt) REVERT: H 59 TYR cc_start: 0.7303 (m-80) cc_final: 0.6397 (m-80) REVERT: H 66 ARG cc_start: 0.6586 (ptt90) cc_final: 0.5644 (ptt90) REVERT: H 67 PHE cc_start: 0.8015 (m-10) cc_final: 0.6890 (m-10) REVERT: H 80 LEU cc_start: 0.7466 (pp) cc_final: 0.7149 (pp) REVERT: H 91 PHE cc_start: 0.6146 (m-80) cc_final: 0.5362 (m-80) REVERT: L 30 ASN cc_start: 0.7772 (t0) cc_final: 0.7318 (t0) REVERT: L 49 TYR cc_start: 0.7609 (p90) cc_final: 0.6747 (p90) REVERT: L 53 ASN cc_start: 0.8461 (m-40) cc_final: 0.7736 (t0) REVERT: L 78 LEU cc_start: 0.7691 (tt) cc_final: 0.7271 (mt) REVERT: L 83 ILE cc_start: 0.8309 (mt) cc_final: 0.7966 (mt) REVERT: L 87 TYR cc_start: 0.6879 (m-80) cc_final: 0.6091 (m-80) REVERT: L 96 THR cc_start: 0.7575 (m) cc_final: 0.7232 (m) REVERT: M 37 ILE cc_start: 0.8828 (mt) cc_final: 0.8505 (tt) REVERT: M 72 ASP cc_start: 0.6644 (t0) cc_final: 0.6210 (t0) REVERT: M 95 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7961 (ttm170) REVERT: N 87 TYR cc_start: 0.6684 (m-80) cc_final: 0.6268 (m-10) REVERT: N 91 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8054 (mt) REVERT: N 98 PHE cc_start: 0.8599 (m-80) cc_final: 0.8378 (m-10) outliers start: 44 outliers final: 29 residues processed: 511 average time/residue: 0.1037 time to fit residues: 68.9195 Evaluate side-chains 512 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 480 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.5980 chunk 49 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.0870 chunk 72 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN E 129 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 30 ASN L 70 HIS M 77 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.102538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.088002 restraints weight = 29396.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.091100 restraints weight = 16659.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.093239 restraints weight = 10835.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.094735 restraints weight = 7654.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095796 restraints weight = 5759.548| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 9419 Z= 0.168 Angle : 0.820 11.304 12798 Z= 0.417 Chirality : 0.050 0.170 1399 Planarity : 0.006 0.048 1643 Dihedral : 6.004 47.689 1293 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.14 % Allowed : 23.34 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.25), residues: 1141 helix: -0.79 (0.38), residues: 154 sheet: 0.22 (0.26), residues: 399 loop : -0.34 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 94 TYR 0.020 0.002 TYR F 27 PHE 0.020 0.002 PHE D 190 TRP 0.028 0.003 TRP F 50 HIS 0.013 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 9402) covalent geometry : angle 0.81566 / 0.42 (12762) SS BOND : bond 0.00514 / 0.28 ( 15) SS BOND : angle 1.58927 / 0.99 ( 30) hydrogen bonds : bond 0.04222 / 2.82 ( 368) hydrogen bonds : angle 6.19731 / 4.38 ( 984) link_NAG-ASN : bond 0.00148 / 0.07 ( 2) link_NAG-ASN : angle 2.48650 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 496 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 VAL cc_start: 0.8568 (p) cc_final: 0.7887 (t) REVERT: B 118 GLN cc_start: 0.8537 (pm20) cc_final: 0.8089 (pm20) REVERT: B 135 MET cc_start: 0.8147 (tmm) cc_final: 0.7815 (tmm) REVERT: B 162 TYR cc_start: 0.6713 (m-80) cc_final: 0.6502 (m-80) REVERT: C 50 ASN cc_start: 0.8219 (t0) cc_final: 0.8015 (t0) REVERT: C 72 GLU cc_start: 0.8162 (tp30) cc_final: 0.7688 (tp30) REVERT: C 92 LYS cc_start: 0.9026 (mttm) cc_final: 0.8769 (mtmm) REVERT: C 97 ASN cc_start: 0.8104 (m-40) cc_final: 0.7763 (m-40) REVERT: C 104 GLU cc_start: 0.7994 (tt0) cc_final: 0.7678 (tt0) REVERT: C 120 TYR cc_start: 0.8739 (m-10) cc_final: 0.8527 (m-10) REVERT: C 147 ASP cc_start: 0.8417 (m-30) cc_final: 0.8056 (m-30) REVERT: C 151 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8038 (mm-30) REVERT: D 100 VAL cc_start: 0.8543 (p) cc_final: 0.8310 (m) REVERT: D 101 GLU cc_start: 0.5941 (pp20) cc_final: 0.5454 (pp20) REVERT: D 119 GLN cc_start: 0.8480 (pt0) cc_final: 0.8236 (pt0) REVERT: D 136 ASN cc_start: 0.7974 (p0) cc_final: 0.7720 (p0) REVERT: D 143 ASP cc_start: 0.8717 (m-30) cc_final: 0.8486 (m-30) REVERT: D 151 MET cc_start: 0.7675 (mtt) cc_final: 0.7363 (mtm) REVERT: D 160 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7652 (mtm110) REVERT: D 165 ASP cc_start: 0.7021 (p0) cc_final: 0.6695 (p0) REVERT: D 209 HIS cc_start: 0.8505 (m90) cc_final: 0.8139 (m90) REVERT: E 23 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8375 (mm-30) REVERT: E 54 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7282 (mm-30) REVERT: E 73 ASN cc_start: 0.8025 (t0) cc_final: 0.7710 (t0) REVERT: E 92 PHE cc_start: 0.8968 (m-80) cc_final: 0.8687 (m-80) REVERT: E 121 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7496 (tm-30) REVERT: E 122 PHE cc_start: 0.8355 (p90) cc_final: 0.7911 (p90) REVERT: E 125 ARG cc_start: 0.7252 (ttm-80) cc_final: 0.6399 (ttt-90) REVERT: F 37 VAL cc_start: 0.8182 (t) cc_final: 0.7796 (m) REVERT: F 38 ARG cc_start: 0.6965 (ptt180) cc_final: 0.6743 (ptt180) REVERT: F 48 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6571 (mtt) REVERT: F 66 ARG cc_start: 0.8457 (mtm110) cc_final: 0.8172 (mtp180) REVERT: F 91 PHE cc_start: 0.7399 (m-10) cc_final: 0.7098 (m-10) REVERT: F 100 TYR cc_start: 0.7087 (t80) cc_final: 0.6748 (t80) REVERT: F 100 MET cc_start: 0.8251 (mtm) cc_final: 0.7753 (mpp) REVERT: G 29 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6844 (m-30) REVERT: G 31 LYS cc_start: 0.8269 (mtmm) cc_final: 0.7966 (mtmm) REVERT: G 54 ARG cc_start: 0.7816 (ttp-110) cc_final: 0.7282 (mtp-110) REVERT: G 60 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8151 (mt-10) REVERT: G 87 TYR cc_start: 0.8205 (m-80) cc_final: 0.7948 (m-80) REVERT: G 105 THR cc_start: 0.4872 (p) cc_final: 0.4650 (p) REVERT: H 27 PHE cc_start: 0.7839 (p90) cc_final: 0.7613 (p90) REVERT: H 34 MET cc_start: 0.7259 (mmm) cc_final: 0.6958 (mmm) REVERT: H 36 TRP cc_start: 0.6649 (m100) cc_final: 0.5906 (m100) REVERT: H 59 TYR cc_start: 0.7416 (m-80) cc_final: 0.6520 (m-80) REVERT: H 80 LEU cc_start: 0.7520 (pp) cc_final: 0.7248 (pp) REVERT: H 91 PHE cc_start: 0.6173 (m-80) cc_final: 0.5395 (m-80) REVERT: L 39 LYS cc_start: 0.7303 (mptt) cc_final: 0.7023 (mptt) REVERT: L 75 ILE cc_start: 0.8064 (mp) cc_final: 0.7784 (mp) REVERT: L 78 LEU cc_start: 0.7744 (tt) cc_final: 0.7284 (mt) REVERT: L 83 ILE cc_start: 0.8186 (mt) cc_final: 0.7931 (mt) REVERT: L 87 TYR cc_start: 0.6792 (m-80) cc_final: 0.6205 (m-80) REVERT: L 90 GLN cc_start: 0.8267 (pp30) cc_final: 0.8026 (pp30) REVERT: L 92 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7303 (tm-30) REVERT: L 93 ASN cc_start: 0.7371 (p0) cc_final: 0.6766 (p0) REVERT: M 38 ARG cc_start: 0.7686 (ptt180) cc_final: 0.7365 (ttp-170) REVERT: M 39 GLN cc_start: 0.8310 (tp40) cc_final: 0.8032 (tp-100) REVERT: M 53 HIS cc_start: 0.8210 (p-80) cc_final: 0.7784 (p-80) REVERT: M 80 LEU cc_start: 0.8557 (tp) cc_final: 0.8260 (mp) REVERT: M 95 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7435 (ttp-110) REVERT: N 24 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7542 (tpp80) REVERT: N 91 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7661 (mp) REVERT: N 98 PHE cc_start: 0.8574 (m-80) cc_final: 0.8350 (m-10) outliers start: 52 outliers final: 34 residues processed: 514 average time/residue: 0.0969 time to fit residues: 65.2693 Evaluate side-chains 511 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 474 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 91 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.0670 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 92 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN E 62 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 37 GLN L 30 ASN L 70 HIS ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.101475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.086884 restraints weight = 29996.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.090000 restraints weight = 16913.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.092113 restraints weight = 10943.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.093597 restraints weight = 7733.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094626 restraints weight = 5825.246| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9419 Z= 0.185 Angle : 0.824 10.669 12798 Z= 0.418 Chirality : 0.051 0.251 1399 Planarity : 0.006 0.051 1643 Dihedral : 6.192 52.480 1293 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 6.33 % Allowed : 25.12 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 1141 helix: -0.75 (0.38), residues: 154 sheet: 0.12 (0.26), residues: 401 loop : -0.41 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 133 TYR 0.023 0.002 TYR F 27 PHE 0.019 0.002 PHE G 98 TRP 0.029 0.003 TRP F 50 HIS 0.012 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 9402) covalent geometry : angle 0.81992 / 0.42 (12762) SS BOND : bond 0.00534 / 0.27 ( 15) SS BOND : angle 1.56468 / 1.01 ( 30) hydrogen bonds : bond 0.04039 / 2.73 ( 368) hydrogen bonds : angle 6.20482 / 4.44 ( 984) link_NAG-ASN : bond 0.00244 / 0.13 ( 2) link_NAG-ASN : angle 2.40927 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 486 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASN cc_start: 0.8858 (m-40) cc_final: 0.8556 (m-40) REVERT: B 118 GLN cc_start: 0.8571 (pm20) cc_final: 0.8098 (pm20) REVERT: B 135 MET cc_start: 0.8013 (tmm) cc_final: 0.7706 (tmm) REVERT: B 162 TYR cc_start: 0.6879 (m-80) cc_final: 0.6593 (m-80) REVERT: C 32 GLU cc_start: 0.2529 (OUTLIER) cc_final: 0.1671 (mp0) REVERT: C 72 GLU cc_start: 0.8097 (tp30) cc_final: 0.7391 (tp30) REVERT: C 76 ILE cc_start: 0.9163 (mt) cc_final: 0.8915 (mm) REVERT: C 80 MET cc_start: 0.6989 (mmt) cc_final: 0.5796 (ttt) REVERT: C 92 LYS cc_start: 0.8958 (mttm) cc_final: 0.8693 (mtmm) REVERT: C 97 ASN cc_start: 0.7988 (m-40) cc_final: 0.7771 (m-40) REVERT: C 104 GLU cc_start: 0.8015 (tt0) cc_final: 0.7754 (tt0) REVERT: C 117 LYS cc_start: 0.8430 (mttt) cc_final: 0.8217 (mttt) REVERT: C 121 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8685 (mp) REVERT: C 131 ARG cc_start: 0.7567 (mmm160) cc_final: 0.7339 (mmm160) REVERT: C 134 ASN cc_start: 0.7866 (t0) cc_final: 0.7216 (t0) REVERT: C 135 LEU cc_start: 0.7678 (mt) cc_final: 0.6556 (mp) REVERT: C 147 ASP cc_start: 0.8402 (m-30) cc_final: 0.8185 (m-30) REVERT: D 89 TYR cc_start: 0.7419 (m-80) cc_final: 0.6646 (m-80) REVERT: D 95 GLU cc_start: 0.8427 (mp0) cc_final: 0.8166 (mt-10) REVERT: D 100 VAL cc_start: 0.8671 (p) cc_final: 0.8257 (m) REVERT: D 101 GLU cc_start: 0.6057 (pp20) cc_final: 0.5474 (pp20) REVERT: D 119 GLN cc_start: 0.8509 (pt0) cc_final: 0.8299 (pt0) REVERT: D 143 ASP cc_start: 0.8725 (m-30) cc_final: 0.8519 (m-30) REVERT: D 151 MET cc_start: 0.7730 (mtt) cc_final: 0.7363 (mtm) REVERT: D 155 GLN cc_start: 0.7561 (tp40) cc_final: 0.6679 (tm-30) REVERT: D 160 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7663 (mtm110) REVERT: D 165 ASP cc_start: 0.7334 (p0) cc_final: 0.6839 (p0) REVERT: D 171 MET cc_start: 0.7362 (mmm) cc_final: 0.6902 (mmm) REVERT: E 23 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8397 (mm-30) REVERT: E 54 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7233 (mm-30) REVERT: E 73 ASN cc_start: 0.8171 (t0) cc_final: 0.7881 (t0) REVERT: E 74 PHE cc_start: 0.8079 (t80) cc_final: 0.7667 (t80) REVERT: E 92 PHE cc_start: 0.8954 (m-10) cc_final: 0.8705 (m-80) REVERT: E 121 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7491 (tm-30) REVERT: E 122 PHE cc_start: 0.8386 (p90) cc_final: 0.7980 (p90) REVERT: E 125 ARG cc_start: 0.7386 (ttm-80) cc_final: 0.6458 (ttt-90) REVERT: F 37 VAL cc_start: 0.8219 (t) cc_final: 0.7743 (m) REVERT: F 59 TYR cc_start: 0.7829 (m-80) cc_final: 0.7217 (m-10) REVERT: F 66 ARG cc_start: 0.8495 (mtm110) cc_final: 0.7982 (mtp180) REVERT: F 71 ARG cc_start: 0.7336 (pmt-80) cc_final: 0.6952 (pmt-80) REVERT: F 91 PHE cc_start: 0.7502 (m-80) cc_final: 0.7184 (m-10) REVERT: F 100 TYR cc_start: 0.7176 (t80) cc_final: 0.6890 (t80) REVERT: F 100 MET cc_start: 0.8262 (mtm) cc_final: 0.7748 (mpp) REVERT: G 4 LEU cc_start: 0.8679 (mt) cc_final: 0.7946 (mm) REVERT: G 31 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7637 (mtmm) REVERT: G 54 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7375 (mtp-110) REVERT: G 60 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7861 (mt-10) REVERT: H 27 PHE cc_start: 0.7885 (p90) cc_final: 0.7307 (p90) REVERT: H 34 MET cc_start: 0.7406 (mmm) cc_final: 0.6963 (mmm) REVERT: H 36 TRP cc_start: 0.6665 (m100) cc_final: 0.5917 (m100) REVERT: H 55 ARG cc_start: 0.8010 (mpp80) cc_final: 0.7679 (mpp80) REVERT: H 59 TYR cc_start: 0.7210 (m-80) cc_final: 0.6557 (m-80) REVERT: H 91 PHE cc_start: 0.6111 (m-80) cc_final: 0.5446 (m-80) REVERT: L 30 ASN cc_start: 0.7933 (t0) cc_final: 0.7548 (t0) REVERT: L 31 GLN cc_start: 0.8448 (mp10) cc_final: 0.8187 (pm20) REVERT: L 32 PHE cc_start: 0.7925 (m-80) cc_final: 0.7660 (m-80) REVERT: L 78 LEU cc_start: 0.7726 (tt) cc_final: 0.7311 (mt) REVERT: L 83 ILE cc_start: 0.8152 (mt) cc_final: 0.7897 (mt) REVERT: L 87 TYR cc_start: 0.6870 (m-80) cc_final: 0.6207 (m-80) REVERT: L 92 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7362 (tm-30) REVERT: L 93 ASN cc_start: 0.7237 (p0) cc_final: 0.6578 (p0) REVERT: M 39 GLN cc_start: 0.8315 (tp40) cc_final: 0.8100 (tp-100) REVERT: M 47 TRP cc_start: 0.7595 (t60) cc_final: 0.6253 (t60) REVERT: M 52 TYR cc_start: 0.7696 (t80) cc_final: 0.7469 (t80) REVERT: M 53 HIS cc_start: 0.8296 (p-80) cc_final: 0.7738 (p-80) REVERT: M 57 THR cc_start: 0.8331 (t) cc_final: 0.8112 (t) REVERT: M 80 LEU cc_start: 0.8517 (tp) cc_final: 0.8276 (mp) REVERT: N 24 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7730 (ttm-80) REVERT: N 75 ILE cc_start: 0.8057 (mp) cc_final: 0.7673 (mm) REVERT: N 87 TYR cc_start: 0.6555 (m-10) cc_final: 0.6327 (m-10) REVERT: N 91 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7755 (mp) outliers start: 64 outliers final: 44 residues processed: 502 average time/residue: 0.1033 time to fit residues: 67.4493 Evaluate side-chains 521 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 474 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 91 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 0.0170 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 18 optimal weight: 0.0570 chunk 67 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 82 optimal weight: 0.0570 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.103057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.088386 restraints weight = 29779.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.091499 restraints weight = 16908.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.093619 restraints weight = 11010.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.095108 restraints weight = 7806.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096185 restraints weight = 5912.814| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9419 Z= 0.149 Angle : 0.835 12.716 12798 Z= 0.412 Chirality : 0.050 0.235 1399 Planarity : 0.006 0.064 1643 Dihedral : 5.825 30.767 1292 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 6.73 % Allowed : 25.72 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.25), residues: 1141 helix: -0.71 (0.39), residues: 154 sheet: 0.14 (0.26), residues: 405 loop : -0.34 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 93 TYR 0.028 0.002 TYR M 34 PHE 0.017 0.002 PHE E 74 TRP 0.045 0.003 TRP G 35 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9402) covalent geometry : angle 0.83255 / 0.41 (12762) SS BOND : bond 0.00464 / 0.26 ( 15) SS BOND : angle 1.28026 / 0.85 ( 30) hydrogen bonds : bond 0.03772 / 2.52 ( 368) hydrogen bonds : angle 5.95956 / 4.25 ( 984) link_NAG-ASN : bond 0.00207 / 0.11 ( 2) link_NAG-ASN : angle 2.25957 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 474 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 VAL cc_start: 0.8869 (m) cc_final: 0.8361 (t) REVERT: B 114 ASN cc_start: 0.8875 (m-40) cc_final: 0.8552 (m-40) REVERT: B 118 GLN cc_start: 0.8545 (pm20) cc_final: 0.8080 (pm20) REVERT: B 135 MET cc_start: 0.7921 (tmm) cc_final: 0.7591 (tmm) REVERT: B 157 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7510 (p0) REVERT: C 72 GLU cc_start: 0.8016 (tp30) cc_final: 0.7391 (tp30) REVERT: C 87 GLN cc_start: 0.8628 (tp40) cc_final: 0.8380 (tp40) REVERT: C 102 TYR cc_start: 0.8037 (t80) cc_final: 0.6925 (t80) REVERT: C 104 GLU cc_start: 0.7825 (tt0) cc_final: 0.7492 (tt0) REVERT: C 134 ASN cc_start: 0.7949 (t0) cc_final: 0.7414 (t0) REVERT: C 151 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7913 (mm-30) REVERT: D 99 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7899 (pp) REVERT: D 101 GLU cc_start: 0.6014 (pp20) cc_final: 0.5542 (pp20) REVERT: D 136 ASN cc_start: 0.8060 (p0) cc_final: 0.7829 (p0) REVERT: D 143 ASP cc_start: 0.8720 (m-30) cc_final: 0.8517 (m-30) REVERT: D 151 MET cc_start: 0.7652 (mtt) cc_final: 0.7331 (mtt) REVERT: D 155 GLN cc_start: 0.7413 (tp40) cc_final: 0.6743 (tm-30) REVERT: D 160 ARG cc_start: 0.8109 (mtm180) cc_final: 0.7653 (mtm-85) REVERT: D 165 ASP cc_start: 0.7383 (p0) cc_final: 0.6958 (p0) REVERT: D 171 MET cc_start: 0.7272 (mmm) cc_final: 0.6753 (mmm) REVERT: D 177 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6292 (mm-30) REVERT: D 212 LEU cc_start: 0.8900 (mm) cc_final: 0.8455 (mp) REVERT: E 23 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8294 (mm-30) REVERT: E 54 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7150 (mm-30) REVERT: E 73 ASN cc_start: 0.8072 (t0) cc_final: 0.7699 (t0) REVERT: E 74 PHE cc_start: 0.7844 (t80) cc_final: 0.7274 (t80) REVERT: E 121 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7519 (tm-30) REVERT: E 122 PHE cc_start: 0.8419 (p90) cc_final: 0.8010 (p90) REVERT: F 37 VAL cc_start: 0.8212 (t) cc_final: 0.7777 (m) REVERT: F 48 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6652 (mtt) REVERT: F 66 ARG cc_start: 0.8396 (mtm110) cc_final: 0.8122 (mtp180) REVERT: F 71 ARG cc_start: 0.7502 (pmt-80) cc_final: 0.7279 (pmt-80) REVERT: F 82 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8494 (tt) REVERT: F 91 PHE cc_start: 0.7473 (m-80) cc_final: 0.7194 (m-10) REVERT: F 100 TYR cc_start: 0.7161 (t80) cc_final: 0.6813 (t80) REVERT: F 100 MET cc_start: 0.8278 (mtm) cc_final: 0.7827 (mpp) REVERT: G 29 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: G 31 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7921 (mtmm) REVERT: G 35 TRP cc_start: 0.7825 (m100) cc_final: 0.6954 (m100) REVERT: G 37 GLN cc_start: 0.7760 (tt0) cc_final: 0.7557 (tt0) REVERT: G 53 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7836 (tptm) REVERT: G 54 ARG cc_start: 0.7541 (ttp-110) cc_final: 0.7017 (mtp-110) REVERT: G 87 TYR cc_start: 0.7996 (m-80) cc_final: 0.7773 (m-80) REVERT: H 27 PHE cc_start: 0.7883 (p90) cc_final: 0.7522 (p90) REVERT: H 34 MET cc_start: 0.7257 (mmm) cc_final: 0.6833 (mmm) REVERT: H 36 TRP cc_start: 0.6632 (m100) cc_final: 0.5886 (m100) REVERT: H 59 TYR cc_start: 0.7341 (m-80) cc_final: 0.6546 (m-10) REVERT: H 91 PHE cc_start: 0.6158 (m-80) cc_final: 0.5539 (m-80) REVERT: L 30 ASN cc_start: 0.7920 (t0) cc_final: 0.7411 (t0) REVERT: L 31 GLN cc_start: 0.8416 (mp10) cc_final: 0.8137 (pm20) REVERT: L 32 PHE cc_start: 0.7842 (m-80) cc_final: 0.7582 (m-80) REVERT: L 49 TYR cc_start: 0.7411 (p90) cc_final: 0.6531 (p90) REVERT: L 53 ASN cc_start: 0.8532 (m110) cc_final: 0.7946 (t0) REVERT: L 78 LEU cc_start: 0.7763 (tt) cc_final: 0.7359 (mt) REVERT: L 87 TYR cc_start: 0.6661 (m-80) cc_final: 0.6169 (m-80) REVERT: L 92 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7349 (tm-30) REVERT: L 93 ASN cc_start: 0.7177 (p0) cc_final: 0.6448 (p0) REVERT: M 2 LEU cc_start: 0.6908 (tp) cc_final: 0.6570 (pt) REVERT: M 38 ARG cc_start: 0.7528 (ptt180) cc_final: 0.7130 (ttp-170) REVERT: M 46 GLN cc_start: 0.7857 (tp40) cc_final: 0.7338 (tp40) REVERT: M 47 TRP cc_start: 0.7365 (t60) cc_final: 0.6118 (t60) REVERT: M 52 TYR cc_start: 0.7513 (t80) cc_final: 0.7083 (t80) REVERT: M 53 HIS cc_start: 0.8294 (p-80) cc_final: 0.7858 (p-80) REVERT: M 80 LEU cc_start: 0.8602 (tp) cc_final: 0.8330 (mp) REVERT: M 95 ARG cc_start: 0.8034 (ptm-80) cc_final: 0.7337 (mtm110) REVERT: N 24 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7561 (ttm-80) REVERT: N 87 TYR cc_start: 0.6573 (m-10) cc_final: 0.6202 (m-10) REVERT: N 91 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7749 (mp) REVERT: N 98 PHE cc_start: 0.8399 (m-80) cc_final: 0.8092 (m-10) REVERT: N 105 ASP cc_start: 0.0419 (OUTLIER) cc_final: 0.0109 (m-30) outliers start: 68 outliers final: 46 residues processed: 492 average time/residue: 0.1014 time to fit residues: 65.5885 Evaluate side-chains 513 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 460 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 74 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN E 62 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN L 70 HIS ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.101209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.086762 restraints weight = 30439.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.089825 restraints weight = 17348.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.091923 restraints weight = 11307.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.093384 restraints weight = 8041.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.094452 restraints weight = 6091.730| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9419 Z= 0.208 Angle : 0.859 12.042 12798 Z= 0.431 Chirality : 0.051 0.210 1399 Planarity : 0.006 0.068 1643 Dihedral : 6.078 36.848 1292 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 7.12 % Allowed : 27.40 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.25), residues: 1141 helix: -0.62 (0.39), residues: 154 sheet: 0.18 (0.26), residues: 395 loop : -0.48 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 93 TYR 0.055 0.003 TYR C 137 PHE 0.017 0.002 PHE E 74 TRP 0.050 0.004 TRP G 35 HIS 0.009 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 9402) covalent geometry : angle 0.85462 / 0.43 (12762) SS BOND : bond 0.00469 / 0.25 ( 15) SS BOND : angle 1.70859 / 1.16 ( 30) hydrogen bonds : bond 0.03901 / 2.63 ( 368) hydrogen bonds : angle 6.14962 / 4.41 ( 984) link_NAG-ASN : bond 0.00028 / 0.01 ( 2) link_NAG-ASN : angle 2.61563 / 1.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 462 time to evaluate : 0.367 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: B 114 ASN cc_start: 0.8804 (m-40) cc_final: 0.8594 (m-40) REVERT: B 118 GLN cc_start: 0.8537 (pm20) cc_final: 0.8114 (pm20) REVERT: B 135 MET cc_start: 0.7971 (tmm) cc_final: 0.7623 (tmm) REVERT: B 157 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7492 (p0) REVERT: B 162 TYR cc_start: 0.6913 (m-80) cc_final: 0.6401 (m-80) REVERT: C 72 GLU cc_start: 0.8058 (tp30) cc_final: 0.7796 (tp30) REVERT: C 80 MET cc_start: 0.7346 (mmt) cc_final: 0.6113 (ttt) REVERT: C 87 GLN cc_start: 0.8621 (tp40) cc_final: 0.8365 (tp40) REVERT: C 104 GLU cc_start: 0.7928 (tt0) cc_final: 0.7576 (tt0) REVERT: C 113 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8464 (mtpp) REVERT: C 120 TYR cc_start: 0.8689 (m-10) cc_final: 0.8175 (m-10) REVERT: C 134 ASN cc_start: 0.7792 (t0) cc_final: 0.7178 (t0) REVERT: D 100 VAL cc_start: 0.8807 (p) cc_final: 0.8328 (m) REVERT: D 136 ASN cc_start: 0.8040 (p0) cc_final: 0.7783 (p0) REVERT: D 151 MET cc_start: 0.7655 (mtt) cc_final: 0.7318 (mtm) REVERT: D 155 GLN cc_start: 0.7410 (tp40) cc_final: 0.6881 (tm-30) REVERT: D 160 ARG cc_start: 0.8043 (mtm180) cc_final: 0.7529 (mtm-85) REVERT: D 165 ASP cc_start: 0.7403 (p0) cc_final: 0.7012 (p0) REVERT: D 171 MET cc_start: 0.7376 (mmm) cc_final: 0.6874 (mmm) REVERT: E 23 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 54 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7190 (mm-30) REVERT: E 73 ASN cc_start: 0.8026 (t0) cc_final: 0.7657 (t0) REVERT: E 122 PHE cc_start: 0.8360 (p90) cc_final: 0.8087 (p90) REVERT: F 48 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6721 (mtt) REVERT: F 66 ARG cc_start: 0.8527 (mtm110) cc_final: 0.8121 (mtp180) REVERT: F 82 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8515 (tt) REVERT: F 91 PHE cc_start: 0.7369 (m-80) cc_final: 0.7045 (m-10) REVERT: F 100 TYR cc_start: 0.7298 (t80) cc_final: 0.6933 (t80) REVERT: F 100 MET cc_start: 0.8277 (mtm) cc_final: 0.7820 (mpp) REVERT: G 29 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6851 (m-30) REVERT: G 31 LYS cc_start: 0.8269 (mtmm) cc_final: 0.7963 (mtmm) REVERT: G 53 LYS cc_start: 0.8314 (mmmm) cc_final: 0.8062 (tmtt) REVERT: G 60 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7742 (mm-30) REVERT: G 83 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: G 98 PHE cc_start: 0.7301 (m-80) cc_final: 0.7080 (m-10) REVERT: H 27 PHE cc_start: 0.7985 (p90) cc_final: 0.7628 (p90) REVERT: H 34 MET cc_start: 0.7259 (mmm) cc_final: 0.6775 (mmm) REVERT: H 36 TRP cc_start: 0.6747 (m100) cc_final: 0.6077 (m100) REVERT: H 59 TYR cc_start: 0.7400 (m-80) cc_final: 0.6238 (m-80) REVERT: H 91 PHE cc_start: 0.6161 (m-80) cc_final: 0.5565 (m-80) REVERT: L 30 ASN cc_start: 0.8008 (t0) cc_final: 0.7532 (t0) REVERT: L 32 PHE cc_start: 0.7870 (m-80) cc_final: 0.7596 (m-80) REVERT: L 49 TYR cc_start: 0.7582 (p90) cc_final: 0.6773 (p90) REVERT: L 53 ASN cc_start: 0.8501 (m110) cc_final: 0.7907 (t0) REVERT: L 70 HIS cc_start: 0.7621 (t70) cc_final: 0.7259 (t-90) REVERT: L 78 LEU cc_start: 0.7729 (tt) cc_final: 0.7336 (mt) REVERT: L 87 TYR cc_start: 0.6820 (m-80) cc_final: 0.6275 (m-80) REVERT: L 92 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7471 (tm-30) REVERT: L 93 ASN cc_start: 0.7247 (p0) cc_final: 0.6469 (p0) REVERT: M 38 ARG cc_start: 0.7564 (ptt180) cc_final: 0.6983 (ttm110) REVERT: M 47 TRP cc_start: 0.7383 (t60) cc_final: 0.6609 (t60) REVERT: M 52 TYR cc_start: 0.7394 (t80) cc_final: 0.7147 (t80) REVERT: M 53 HIS cc_start: 0.8350 (p-80) cc_final: 0.7834 (p-80) REVERT: M 80 LEU cc_start: 0.8533 (tp) cc_final: 0.8308 (mp) REVERT: N 24 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7679 (ttm-80) REVERT: N 75 ILE cc_start: 0.8052 (mp) cc_final: 0.7672 (mm) REVERT: N 91 LEU cc_start: 0.8187 (mt) cc_final: 0.7687 (mp) REVERT: N 96 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.7828 (t0) outliers start: 72 outliers final: 55 residues processed: 488 average time/residue: 0.1015 time to fit residues: 65.0506 Evaluate side-chains 517 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 456 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 96 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 90 optimal weight: 0.0570 chunk 64 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 74 optimal weight: 0.0870 chunk 37 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 123 GLN E 62 ASN G 52 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.104334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.090133 restraints weight = 30169.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.093145 restraints weight = 17406.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095192 restraints weight = 11410.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.096554 restraints weight = 8145.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.097637 restraints weight = 6235.797| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9419 Z= 0.151 Angle : 0.870 14.847 12798 Z= 0.428 Chirality : 0.050 0.167 1399 Planarity : 0.006 0.071 1643 Dihedral : 5.875 31.739 1292 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 5.93 % Allowed : 29.48 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.25), residues: 1141 helix: -0.75 (0.39), residues: 154 sheet: 0.20 (0.27), residues: 392 loop : -0.52 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 108 TYR 0.028 0.002 TYR F 27 PHE 0.029 0.002 PHE E 74 TRP 0.059 0.003 TRP G 35 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9402) covalent geometry : angle 0.86553 / 0.43 (12762) SS BOND : bond 0.00398 / 0.22 ( 15) SS BOND : angle 1.83112 / 1.15 ( 30) hydrogen bonds : bond 0.03753 / 2.50 ( 368) hydrogen bonds : angle 5.86206 / 4.18 ( 984) link_NAG-ASN : bond 0.00115 / 0.06 ( 2) link_NAG-ASN : angle 2.17520 / 1.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 470 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASN cc_start: 0.8747 (m-40) cc_final: 0.8533 (m-40) REVERT: B 118 GLN cc_start: 0.8455 (pm20) cc_final: 0.8104 (pm20) REVERT: B 157 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7517 (p0) REVERT: C 72 GLU cc_start: 0.7887 (tp30) cc_final: 0.7597 (tp30) REVERT: C 80 MET cc_start: 0.7184 (mmt) cc_final: 0.6076 (mtp) REVERT: C 87 GLN cc_start: 0.8594 (tp40) cc_final: 0.8378 (tp40) REVERT: C 104 GLU cc_start: 0.7736 (tt0) cc_final: 0.7400 (tt0) REVERT: D 95 GLU cc_start: 0.8287 (mp0) cc_final: 0.8034 (mt-10) REVERT: D 102 ARG cc_start: 0.8027 (tmm-80) cc_final: 0.7781 (ttp80) REVERT: D 119 GLN cc_start: 0.8280 (pt0) cc_final: 0.7810 (pm20) REVERT: D 136 ASN cc_start: 0.7963 (p0) cc_final: 0.7709 (p0) REVERT: D 151 MET cc_start: 0.7546 (mtt) cc_final: 0.7289 (mtm) REVERT: D 155 GLN cc_start: 0.7509 (tp40) cc_final: 0.6891 (tm-30) REVERT: D 160 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7441 (mtm-85) REVERT: D 165 ASP cc_start: 0.7433 (p0) cc_final: 0.7046 (p0) REVERT: D 171 MET cc_start: 0.7172 (mmm) cc_final: 0.6720 (mmm) REVERT: D 209 HIS cc_start: 0.8264 (m90) cc_final: 0.7912 (m90) REVERT: E 23 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8275 (mm-30) REVERT: E 54 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7073 (mm-30) REVERT: E 62 ASN cc_start: 0.8342 (m-40) cc_final: 0.8110 (m-40) REVERT: E 73 ASN cc_start: 0.7901 (t0) cc_final: 0.7582 (t0) REVERT: E 92 PHE cc_start: 0.8783 (m-10) cc_final: 0.8437 (m-80) REVERT: E 122 PHE cc_start: 0.8340 (p90) cc_final: 0.8127 (p90) REVERT: F 48 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6554 (mtt) REVERT: F 66 ARG cc_start: 0.8380 (mtm110) cc_final: 0.8043 (mtp180) REVERT: F 82 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8593 (tt) REVERT: F 91 PHE cc_start: 0.7480 (m-80) cc_final: 0.7129 (m-10) REVERT: F 100 TYR cc_start: 0.7123 (t80) cc_final: 0.6797 (t80) REVERT: F 100 MET cc_start: 0.8249 (mtm) cc_final: 0.7905 (mpp) REVERT: G 29 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6372 (m-30) REVERT: G 31 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8139 (mtmm) REVERT: G 53 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7759 (tptm) REVERT: G 60 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7607 (mm-30) REVERT: H 27 PHE cc_start: 0.7783 (p90) cc_final: 0.7375 (p90) REVERT: H 34 MET cc_start: 0.7064 (mmm) cc_final: 0.6629 (mmm) REVERT: H 36 TRP cc_start: 0.6459 (m100) cc_final: 0.5772 (m100) REVERT: H 59 TYR cc_start: 0.7379 (m-80) cc_final: 0.6224 (m-80) REVERT: H 91 PHE cc_start: 0.6023 (m-80) cc_final: 0.5403 (m-80) REVERT: L 30 ASN cc_start: 0.7862 (t0) cc_final: 0.7564 (t0) REVERT: L 31 GLN cc_start: 0.8362 (mp10) cc_final: 0.7959 (pm20) REVERT: L 49 TYR cc_start: 0.7526 (p90) cc_final: 0.6633 (p90) REVERT: L 53 ASN cc_start: 0.8441 (m110) cc_final: 0.7937 (t0) REVERT: L 70 HIS cc_start: 0.7312 (t70) cc_final: 0.6964 (t-90) REVERT: L 82 ASP cc_start: 0.8543 (m-30) cc_final: 0.8289 (m-30) REVERT: L 87 TYR cc_start: 0.6657 (m-80) cc_final: 0.6276 (m-80) REVERT: L 89 GLN cc_start: 0.7879 (pt0) cc_final: 0.7457 (pt0) REVERT: M 38 ARG cc_start: 0.7459 (ptt180) cc_final: 0.6777 (ttm-80) REVERT: M 46 GLN cc_start: 0.7880 (tp40) cc_final: 0.7513 (tp40) REVERT: M 47 TRP cc_start: 0.7242 (t60) cc_final: 0.5792 (t60) REVERT: M 80 LEU cc_start: 0.8472 (tp) cc_final: 0.8237 (mp) REVERT: M 90 TYR cc_start: 0.7214 (m-10) cc_final: 0.6970 (m-10) REVERT: M 95 ARG cc_start: 0.7965 (ptm-80) cc_final: 0.7191 (mtm110) REVERT: N 2 ILE cc_start: 0.8273 (mm) cc_final: 0.8065 (mm) REVERT: N 89 GLN cc_start: 0.7019 (tm-30) cc_final: 0.6803 (tm-30) outliers start: 60 outliers final: 45 residues processed: 489 average time/residue: 0.1022 time to fit residues: 65.5421 Evaluate side-chains 501 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 451 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 37 GLN G 52 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.101554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.086946 restraints weight = 30058.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.090026 restraints weight = 17064.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.092131 restraints weight = 11138.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.093596 restraints weight = 7943.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.094617 restraints weight = 6045.091| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9419 Z= 0.193 Angle : 0.890 15.144 12798 Z= 0.441 Chirality : 0.052 0.291 1399 Planarity : 0.006 0.055 1643 Dihedral : 6.079 34.355 1292 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 6.33 % Allowed : 28.98 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1141 helix: -0.65 (0.40), residues: 153 sheet: 0.15 (0.26), residues: 395 loop : -0.56 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 168 TYR 0.037 0.003 TYR B 162 PHE 0.033 0.003 PHE D 74 TRP 0.056 0.004 TRP G 35 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 ( 9402) covalent geometry : angle 0.88609 / 0.44 (12762) SS BOND : bond 0.00557 / 0.30 ( 15) SS BOND : angle 1.72596 / 1.12 ( 30) hydrogen bonds : bond 0.03890 / 2.61 ( 368) hydrogen bonds : angle 6.03316 / 4.30 ( 984) link_NAG-ASN : bond 0.00050 / 0.03 ( 2) link_NAG-ASN : angle 2.43214 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 460 time to evaluate : 0.266 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: B 109 LEU cc_start: 0.8760 (mm) cc_final: 0.8308 (pp) REVERT: B 114 ASN cc_start: 0.8779 (m-40) cc_final: 0.8547 (m-40) REVERT: B 118 GLN cc_start: 0.8476 (pm20) cc_final: 0.8102 (pm20) REVERT: B 157 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7732 (p0) REVERT: C 72 GLU cc_start: 0.7983 (tp30) cc_final: 0.7662 (tp30) REVERT: C 86 ARG cc_start: 0.8916 (mmm-85) cc_final: 0.8670 (mmt180) REVERT: C 87 GLN cc_start: 0.8619 (tp40) cc_final: 0.8359 (tp40) REVERT: C 104 GLU cc_start: 0.7954 (tt0) cc_final: 0.7542 (tt0) REVERT: D 102 ARG cc_start: 0.7952 (tmm-80) cc_final: 0.7716 (ttp80) REVERT: D 136 ASN cc_start: 0.8052 (p0) cc_final: 0.7805 (p0) REVERT: D 151 MET cc_start: 0.7649 (mtt) cc_final: 0.7356 (mtt) REVERT: D 155 GLN cc_start: 0.7444 (tp40) cc_final: 0.6816 (tm-30) REVERT: D 165 ASP cc_start: 0.7543 (p0) cc_final: 0.7166 (p0) REVERT: D 171 MET cc_start: 0.7436 (mmm) cc_final: 0.7013 (mmm) REVERT: D 177 GLU cc_start: 0.6583 (mm-30) cc_final: 0.6030 (mm-30) REVERT: D 209 HIS cc_start: 0.8387 (m90) cc_final: 0.8043 (m90) REVERT: E 23 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8280 (mm-30) REVERT: E 54 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7153 (mm-30) REVERT: E 73 ASN cc_start: 0.7994 (t0) cc_final: 0.7631 (t0) REVERT: F 3 GLN cc_start: 0.7768 (pm20) cc_final: 0.7521 (pm20) REVERT: F 66 ARG cc_start: 0.8475 (mtm110) cc_final: 0.8054 (mtp180) REVERT: F 82 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8555 (tt) REVERT: F 91 PHE cc_start: 0.7540 (m-80) cc_final: 0.7168 (m-10) REVERT: F 100 TYR cc_start: 0.7254 (t80) cc_final: 0.6898 (t80) REVERT: F 100 MET cc_start: 0.8291 (mtm) cc_final: 0.7901 (mpp) REVERT: G 29 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6488 (m-30) REVERT: G 31 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8027 (mtmm) REVERT: G 53 LYS cc_start: 0.8326 (mmmm) cc_final: 0.7950 (tptp) REVERT: G 54 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7182 (mtp-110) REVERT: H 27 PHE cc_start: 0.7956 (p90) cc_final: 0.7575 (p90) REVERT: H 34 MET cc_start: 0.7225 (mmm) cc_final: 0.6962 (mmm) REVERT: H 36 TRP cc_start: 0.6509 (m100) cc_final: 0.5803 (m100) REVERT: H 59 TYR cc_start: 0.7571 (m-80) cc_final: 0.6288 (m-80) REVERT: H 91 PHE cc_start: 0.6102 (m-80) cc_final: 0.5508 (m-80) REVERT: L 30 ASN cc_start: 0.7941 (t0) cc_final: 0.7616 (t0) REVERT: L 31 GLN cc_start: 0.8404 (mp10) cc_final: 0.8018 (pm20) REVERT: L 53 ASN cc_start: 0.8461 (m110) cc_final: 0.7979 (t0) REVERT: L 87 TYR cc_start: 0.6714 (m-80) cc_final: 0.6120 (m-80) REVERT: L 89 GLN cc_start: 0.8067 (pt0) cc_final: 0.7596 (pt0) REVERT: M 38 ARG cc_start: 0.7526 (ptt180) cc_final: 0.6848 (ttm-80) REVERT: M 46 GLN cc_start: 0.7910 (tp40) cc_final: 0.7598 (tp40) REVERT: M 47 TRP cc_start: 0.7320 (t60) cc_final: 0.6135 (t60) REVERT: M 52 TYR cc_start: 0.7142 (t80) cc_final: 0.6518 (t80) REVERT: M 63 PHE cc_start: 0.8270 (m-10) cc_final: 0.8067 (m-10) REVERT: M 80 LEU cc_start: 0.8637 (tp) cc_final: 0.8383 (mp) REVERT: M 82 VAL cc_start: 0.8768 (t) cc_final: 0.8558 (p) REVERT: M 97 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6247 (mtm180) REVERT: N 2 ILE cc_start: 0.8207 (mm) cc_final: 0.7936 (pt) REVERT: N 24 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7281 (tpp-160) REVERT: N 48 ILE cc_start: 0.7771 (mm) cc_final: 0.7386 (mm) REVERT: N 75 ILE cc_start: 0.8028 (mp) cc_final: 0.7661 (mm) REVERT: N 91 LEU cc_start: 0.7954 (mt) cc_final: 0.7707 (mt) outliers start: 64 outliers final: 50 residues processed: 480 average time/residue: 0.1038 time to fit residues: 65.5910 Evaluate side-chains 503 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 449 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 94 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 37 GLN G 52 ASN L 70 HIS L 93 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 ASN N 97 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.101648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.087606 restraints weight = 30132.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.090626 restraints weight = 17271.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.092652 restraints weight = 11302.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.094127 restraints weight = 8071.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.095151 restraints weight = 6110.896| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9419 Z= 0.212 Angle : 0.939 15.416 12798 Z= 0.468 Chirality : 0.053 0.277 1399 Planarity : 0.007 0.114 1643 Dihedral : 6.301 38.098 1292 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.49 % Favored : 93.43 % Rotamer: Outliers : 6.53 % Allowed : 29.67 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1141 helix: -0.53 (0.40), residues: 153 sheet: 0.08 (0.27), residues: 386 loop : -0.66 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 168 TYR 0.038 0.003 TYR B 162 PHE 0.038 0.003 PHE D 74 TRP 0.061 0.004 TRP G 35 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 9402) covalent geometry : angle 0.93277 / 0.47 (12762) SS BOND : bond 0.00652 / 0.32 ( 15) SS BOND : angle 2.16775 / 1.42 ( 30) hydrogen bonds : bond 0.03931 / 2.64 ( 368) hydrogen bonds : angle 6.20950 / 4.44 ( 984) link_NAG-ASN : bond 0.00143 / 0.07 ( 2) link_NAG-ASN : angle 2.53160 / 1.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 449 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8736 (mm) cc_final: 0.8275 (pp) REVERT: B 114 ASN cc_start: 0.8777 (m-40) cc_final: 0.8536 (m-40) REVERT: B 118 GLN cc_start: 0.8477 (pm20) cc_final: 0.8075 (pm20) REVERT: B 157 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7719 (p0) REVERT: C 32 GLU cc_start: 0.3012 (OUTLIER) cc_final: 0.2366 (mp0) REVERT: C 72 GLU cc_start: 0.7979 (tp30) cc_final: 0.7657 (tp30) REVERT: C 87 GLN cc_start: 0.8634 (tp40) cc_final: 0.8419 (tp40) REVERT: C 104 GLU cc_start: 0.7941 (tt0) cc_final: 0.7592 (tt0) REVERT: D 151 MET cc_start: 0.7587 (mtt) cc_final: 0.7255 (mtm) REVERT: D 165 ASP cc_start: 0.7501 (p0) cc_final: 0.7158 (p0) REVERT: D 171 MET cc_start: 0.7239 (mmm) cc_final: 0.6813 (mmm) REVERT: D 177 GLU cc_start: 0.6638 (mm-30) cc_final: 0.6083 (mm-30) REVERT: D 209 HIS cc_start: 0.8421 (m90) cc_final: 0.8083 (m90) REVERT: E 23 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8264 (mm-30) REVERT: E 54 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7170 (mm-30) REVERT: E 73 ASN cc_start: 0.8046 (t0) cc_final: 0.7670 (t0) REVERT: E 74 PHE cc_start: 0.7171 (t80) cc_final: 0.6846 (t80) REVERT: E 78 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8606 (ttmt) REVERT: F 3 GLN cc_start: 0.7695 (pm20) cc_final: 0.7456 (pm20) REVERT: F 66 ARG cc_start: 0.8427 (mtm110) cc_final: 0.7982 (mtp180) REVERT: F 82 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8584 (tt) REVERT: F 91 PHE cc_start: 0.7544 (m-80) cc_final: 0.7202 (m-10) REVERT: F 100 TYR cc_start: 0.7196 (t80) cc_final: 0.6841 (t80) REVERT: F 100 MET cc_start: 0.8235 (mtm) cc_final: 0.7846 (mpp) REVERT: G 29 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6478 (m-30) REVERT: G 31 LYS cc_start: 0.8351 (mtmm) cc_final: 0.7934 (mtmm) REVERT: G 37 GLN cc_start: 0.7540 (tt0) cc_final: 0.7107 (tt0) REVERT: G 53 LYS cc_start: 0.8327 (mmmm) cc_final: 0.7856 (tptm) REVERT: G 54 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7074 (mtp-110) REVERT: G 81 MET cc_start: 0.7643 (ppp) cc_final: 0.7374 (ppp) REVERT: H 27 PHE cc_start: 0.7943 (p90) cc_final: 0.7597 (p90) REVERT: H 34 MET cc_start: 0.7120 (mmm) cc_final: 0.6868 (mmm) REVERT: H 36 TRP cc_start: 0.6435 (m100) cc_final: 0.5759 (m100) REVERT: H 59 TYR cc_start: 0.7588 (m-80) cc_final: 0.6245 (m-80) REVERT: H 91 PHE cc_start: 0.6010 (m-80) cc_final: 0.5419 (m-80) REVERT: L 30 ASN cc_start: 0.7970 (t0) cc_final: 0.7657 (t0) REVERT: L 31 GLN cc_start: 0.8355 (mp10) cc_final: 0.8013 (pm20) REVERT: L 53 ASN cc_start: 0.8344 (m110) cc_final: 0.7921 (t0) REVERT: L 70 HIS cc_start: 0.7619 (t70) cc_final: 0.7198 (t-90) REVERT: L 75 ILE cc_start: 0.7949 (mp) cc_final: 0.7692 (mp) REVERT: L 87 TYR cc_start: 0.6739 (m-80) cc_final: 0.6158 (m-80) REVERT: L 89 GLN cc_start: 0.8014 (pt0) cc_final: 0.7499 (pt0) REVERT: M 46 GLN cc_start: 0.8003 (tp40) cc_final: 0.7681 (tp40) REVERT: N 46 LEU cc_start: 0.8689 (tp) cc_final: 0.8204 (pp) REVERT: N 48 ILE cc_start: 0.7802 (mm) cc_final: 0.7326 (mm) REVERT: N 75 ILE cc_start: 0.8029 (mp) cc_final: 0.7669 (mm) REVERT: N 91 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7665 (mt) REVERT: N 105 ASP cc_start: 0.1417 (OUTLIER) cc_final: 0.1013 (m-30) outliers start: 66 outliers final: 52 residues processed: 471 average time/residue: 0.1124 time to fit residues: 69.9383 Evaluate side-chains 501 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 443 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 chunk 107 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 52 ASN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.101710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.087595 restraints weight = 30188.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.090661 restraints weight = 17273.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.092740 restraints weight = 11283.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.094214 restraints weight = 8016.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.095279 restraints weight = 6050.020| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.270 9419 Z= 0.308 Angle : 1.322 59.200 12798 Z= 0.746 Chirality : 0.054 0.345 1399 Planarity : 0.007 0.116 1643 Dihedral : 6.323 38.197 1292 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 27.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.40 % Favored : 93.51 % Rotamer: Outliers : 6.03 % Allowed : 29.97 % Favored : 64.00 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.25), residues: 1141 helix: -0.53 (0.40), residues: 153 sheet: 0.08 (0.27), residues: 386 loop : -0.68 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 131 TYR 0.032 0.003 TYR F 27 PHE 0.035 0.003 PHE D 74 TRP 0.053 0.004 TRP G 35 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.31 ( 9402) covalent geometry : angle 1.30712 / 0.74 (12762) SS BOND : bond 0.01099 / 0.45 ( 15) SS BOND : angle 4.15045 / 2.68 ( 30) hydrogen bonds : bond 0.04086 / 2.67 ( 368) hydrogen bonds : angle 6.20648 / 4.43 ( 984) link_NAG-ASN : bond 0.00171 / 0.09 ( 2) link_NAG-ASN : angle 2.49669 / 1.46 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 441 time to evaluate : 0.361 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: B 114 ASN cc_start: 0.8774 (m-40) cc_final: 0.8529 (m-40) REVERT: B 118 GLN cc_start: 0.8468 (pm20) cc_final: 0.8080 (pm20) REVERT: B 157 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7713 (p0) REVERT: C 32 GLU cc_start: 0.2965 (OUTLIER) cc_final: 0.2339 (mp0) REVERT: C 72 GLU cc_start: 0.7947 (tp30) cc_final: 0.7642 (tp30) REVERT: C 80 MET cc_start: 0.7323 (mmt) cc_final: 0.6109 (ttm) REVERT: C 87 GLN cc_start: 0.8623 (tp40) cc_final: 0.8401 (tp40) REVERT: C 104 GLU cc_start: 0.7925 (tt0) cc_final: 0.7578 (tt0) REVERT: D 151 MET cc_start: 0.7569 (mtt) cc_final: 0.7223 (mtm) REVERT: D 165 ASP cc_start: 0.7497 (p0) cc_final: 0.7146 (p0) REVERT: D 171 MET cc_start: 0.7210 (mmm) cc_final: 0.6761 (mmm) REVERT: D 177 GLU cc_start: 0.6633 (mm-30) cc_final: 0.6070 (mm-30) REVERT: D 209 HIS cc_start: 0.8390 (m90) cc_final: 0.8060 (m90) REVERT: E 23 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8257 (mm-30) REVERT: E 54 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7141 (mm-30) REVERT: E 73 ASN cc_start: 0.8014 (t0) cc_final: 0.7660 (t0) REVERT: E 74 PHE cc_start: 0.7162 (t80) cc_final: 0.6851 (t80) REVERT: E 78 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8589 (ttmt) REVERT: F 3 GLN cc_start: 0.7689 (pm20) cc_final: 0.7466 (pm20) REVERT: F 66 ARG cc_start: 0.8418 (mtm110) cc_final: 0.7978 (mtp180) REVERT: F 82 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8588 (tt) REVERT: F 91 PHE cc_start: 0.7559 (m-80) cc_final: 0.7202 (m-10) REVERT: F 100 TYR cc_start: 0.7194 (t80) cc_final: 0.6881 (t80) REVERT: F 100 MET cc_start: 0.8230 (mtm) cc_final: 0.7847 (mpp) REVERT: G 29 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6466 (m-30) REVERT: G 31 LYS cc_start: 0.8309 (mtmm) cc_final: 0.8070 (mtmm) REVERT: G 37 GLN cc_start: 0.7505 (tt0) cc_final: 0.7159 (tt0) REVERT: G 53 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7828 (tptm) REVERT: G 54 ARG cc_start: 0.7563 (ttp-110) cc_final: 0.7039 (mtp-110) REVERT: G 81 MET cc_start: 0.7640 (ppp) cc_final: 0.7370 (ppp) REVERT: H 27 PHE cc_start: 0.7907 (p90) cc_final: 0.7561 (p90) REVERT: H 34 MET cc_start: 0.7099 (mmm) cc_final: 0.6856 (mmm) REVERT: H 36 TRP cc_start: 0.6405 (m100) cc_final: 0.5798 (m100) REVERT: H 59 TYR cc_start: 0.7575 (m-80) cc_final: 0.6237 (m-80) REVERT: H 91 PHE cc_start: 0.5994 (m-80) cc_final: 0.5441 (m-80) REVERT: L 30 ASN cc_start: 0.7958 (t0) cc_final: 0.7647 (t0) REVERT: L 31 GLN cc_start: 0.8331 (mp10) cc_final: 0.7998 (pm20) REVERT: L 53 ASN cc_start: 0.8341 (m110) cc_final: 0.7891 (t0) REVERT: L 70 HIS cc_start: 0.7579 (t70) cc_final: 0.7164 (t-90) REVERT: L 87 TYR cc_start: 0.6713 (m-80) cc_final: 0.6152 (m-80) REVERT: L 89 GLN cc_start: 0.8008 (pt0) cc_final: 0.7495 (pt0) REVERT: M 38 ARG cc_start: 0.7491 (ptt180) cc_final: 0.6888 (ttm-80) REVERT: M 46 GLN cc_start: 0.8009 (tp40) cc_final: 0.7723 (tp40) REVERT: M 80 LEU cc_start: 0.7977 (mp) cc_final: 0.7493 (mp) REVERT: N 46 LEU cc_start: 0.8685 (tp) cc_final: 0.8191 (pp) REVERT: N 48 ILE cc_start: 0.7782 (mm) cc_final: 0.7330 (mm) REVERT: N 75 ILE cc_start: 0.8022 (mp) cc_final: 0.7663 (mm) REVERT: N 105 ASP cc_start: 0.1382 (OUTLIER) cc_final: 0.0990 (m-30) outliers start: 61 outliers final: 51 residues processed: 460 average time/residue: 0.1113 time to fit residues: 67.7339 Evaluate side-chains 498 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 441 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.0060 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 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 = 0.3807 r_free = 0.3807 target = 0.101678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.087619 restraints weight = 29747.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.090629 restraints weight = 17023.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.092704 restraints weight = 11127.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.094150 restraints weight = 7917.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095194 restraints weight = 5991.641| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.312 9419 Z= 0.347 Angle : 1.339 57.880 12798 Z= 0.755 Chirality : 0.054 0.345 1399 Planarity : 0.007 0.116 1643 Dihedral : 6.323 38.197 1292 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 29.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.40 % Favored : 93.51 % Rotamer: Outliers : 5.64 % Allowed : 30.37 % Favored : 64.00 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.25), residues: 1141 helix: -0.53 (0.40), residues: 153 sheet: 0.08 (0.27), residues: 386 loop : -0.68 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 131 TYR 0.032 0.003 TYR F 27 PHE 0.035 0.003 PHE D 74 TRP 0.053 0.004 TRP G 35 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.31 ( 9402) covalent geometry : angle 1.30402 / 0.74 (12762) SS BOND : bond 0.08133 / 3.23 ( 15) SS BOND : angle 6.34781 / 4.66 ( 30) hydrogen bonds : bond 0.04086 / 2.67 ( 368) hydrogen bonds : angle 6.20648 / 4.43 ( 984) link_NAG-ASN : bond 0.00171 / 0.09 ( 2) link_NAG-ASN : angle 2.49669 / 1.46 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.95 seconds wall clock time: 38 minutes 44.57 seconds (2324.57 seconds total)