Starting phenix.real_space_refine on Wed Mar 4 03:39:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m30_23640/03_2026/7m30_23640.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m30_23640/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m30_23640/03_2026/7m30_23640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m30_23640/03_2026/7m30_23640.map" model { file = "/net/cci-nas-00/data/ceres_data/7m30_23640/03_2026/7m30_23640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m30_23640/03_2026/7m30_23640.cif" } 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-5986/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.47, per 1000 atoms: 0.27 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: 0.78 Conformation dependent library (CDL) restraints added in 337.9 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: 0.50 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: 1.41 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: 5135 17.43 - 34.85: 384 34.85 - 52.27: 95 52.27 - 69.70: 23 69.70 - 87.12: 11 Dihedral angle restraints: 5648 sinusoidal: 2263 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 5645 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: 7.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 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 : 13.640 87.119 3439 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 covalent geometry : bond 0.00538 ( 9402) covalent geometry : angle 1.15137 (12762) SS BOND : bond 0.00843 ( 15) SS BOND : angle 3.30662 ( 30) hydrogen bonds : bond 0.13648 ( 368) hydrogen bonds : angle 7.46840 ( 984) link_NAG-ASN : bond 0.00327 ( 2) link_NAG-ASN : angle 3.30815 ( 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 : 0.366 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: 0.7897 (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: 0.1255 time to fit residues: 88.8823 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 : 0.354 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.102063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.087532 restraints weight = 29932.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.090586 restraints weight = 16962.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.092685 restraints weight = 11042.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.094155 restraints weight = 7833.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.095246 restraints weight = 5912.657| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 9419 Z= 0.211 Angle : 0.876 12.913 12798 Z= 0.451 Chirality : 0.052 0.205 1399 Planarity : 0.006 0.061 1643 Dihedral : 6.741 59.898 1341 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.35 % Allowed : 20.08 % Favored : 75.57 % 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: -0.88 (0.38), residues: 155 sheet: 0.13 (0.25), residues: 407 loop : -0.23 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 38 TYR 0.028 0.003 TYR D 56 PHE 0.030 0.003 PHE D 147 TRP 0.027 0.003 TRP F 47 HIS 0.013 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 9402) covalent geometry : angle 0.87044 (12762) SS BOND : bond 0.00645 ( 15) SS BOND : angle 1.98534 ( 30) hydrogen bonds : bond 0.05004 ( 368) hydrogen bonds : angle 6.50558 ( 984) link_NAG-ASN : bond 0.00069 ( 2) link_NAG-ASN : angle 2.71942 ( 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 547 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 503 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ARG cc_start: 0.7787 (mpt180) cc_final: 0.7546 (mpt180) REVERT: B 99 VAL cc_start: 0.8624 (p) cc_final: 0.8251 (t) REVERT: B 114 ASN cc_start: 0.8825 (m-40) cc_final: 0.8556 (m-40) REVERT: B 118 GLN cc_start: 0.8580 (pm20) cc_final: 0.8192 (pm20) REVERT: B 133 ARG cc_start: 0.8684 (ttp-170) cc_final: 0.8421 (ttt180) REVERT: B 135 MET cc_start: 0.8255 (tmm) cc_final: 0.7958 (tmm) REVERT: B 136 THR cc_start: 0.8756 (m) cc_final: 0.8523 (p) REVERT: B 162 TYR cc_start: 0.6895 (m-80) cc_final: 0.6654 (m-80) REVERT: C 32 GLU cc_start: 0.2985 (OUTLIER) cc_final: 0.2409 (mp0) REVERT: C 44 TYR cc_start: 0.7993 (p90) cc_final: 0.7531 (p90) REVERT: C 48 MET cc_start: 0.8453 (mpp) cc_final: 0.8228 (mmp) REVERT: C 72 GLU cc_start: 0.8250 (tp30) cc_final: 0.7566 (tp30) REVERT: C 74 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8096 (ttp80) REVERT: C 76 ILE cc_start: 0.9181 (mt) cc_final: 0.8942 (mm) REVERT: C 85 THR cc_start: 0.8445 (t) cc_final: 0.7721 (m) REVERT: C 91 ASN cc_start: 0.8904 (m-40) cc_final: 0.8615 (m-40) REVERT: C 92 LYS cc_start: 0.9133 (mttm) cc_final: 0.8921 (mttp) REVERT: C 97 ASN cc_start: 0.8196 (m-40) cc_final: 0.7910 (m-40) REVERT: C 104 GLU cc_start: 0.8143 (tt0) cc_final: 0.7759 (tt0) REVERT: C 130 TYR cc_start: 0.8619 (p90) cc_final: 0.8413 (p90) REVERT: C 147 ASP cc_start: 0.8551 (m-30) cc_final: 0.8097 (m-30) REVERT: D 99 LEU cc_start: 0.8314 (tt) cc_final: 0.7879 (pp) REVERT: D 119 GLN cc_start: 0.8412 (pt0) cc_final: 0.8180 (pt0) REVERT: D 136 ASN cc_start: 0.8024 (p0) cc_final: 0.7782 (p0) REVERT: D 143 ASP cc_start: 0.8731 (m-30) cc_final: 0.8528 (m-30) REVERT: D 151 MET cc_start: 0.7696 (mtm) cc_final: 0.7279 (mtm) REVERT: D 160 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7615 (mtm110) REVERT: D 191 GLN cc_start: 0.7908 (pt0) cc_final: 0.7633 (pt0) REVERT: D 193 ARG cc_start: 0.8450 (ptp-110) cc_final: 0.8244 (ptp-110) REVERT: D 212 LEU cc_start: 0.8890 (mm) cc_final: 0.8539 (mp) REVERT: E 23 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8313 (mm-30) REVERT: E 44 LEU cc_start: 0.8962 (mp) cc_final: 0.8760 (mp) REVERT: E 51 LYS cc_start: 0.9127 (tttt) cc_final: 0.8916 (tttm) REVERT: E 54 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7320 (mm-30) REVERT: E 71 LEU cc_start: 0.8844 (mm) cc_final: 0.8638 (mt) REVERT: E 73 ASN cc_start: 0.8005 (t0) cc_final: 0.7799 (t0) REVERT: E 121 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7503 (tm-30) REVERT: E 122 PHE cc_start: 0.8306 (p90) cc_final: 0.7919 (p90) REVERT: E 125 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.6447 (ttt-90) REVERT: F 37 VAL cc_start: 0.8304 (t) cc_final: 0.7858 (m) REVERT: F 66 ARG cc_start: 0.8287 (mtm110) cc_final: 0.7768 (mtp180) REVERT: F 82 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8459 (tt) REVERT: F 91 PHE cc_start: 0.7471 (m-10) cc_final: 0.7212 (m-10) REVERT: F 100 TYR cc_start: 0.7202 (t80) cc_final: 0.6825 (t80) REVERT: G 27 ARG cc_start: 0.8417 (ptt-90) cc_final: 0.7969 (ptt-90) REVERT: G 31 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8102 (mtmm) REVERT: G 37 GLN cc_start: 0.7632 (tt0) cc_final: 0.7394 (tt0) REVERT: G 54 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7295 (mtp-110) REVERT: G 60 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7860 (mt-10) REVERT: G 105 THR cc_start: 0.5439 (p) cc_final: 0.4772 (p) REVERT: H 27 PHE cc_start: 0.7857 (p90) cc_final: 0.7414 (p90) REVERT: H 36 TRP cc_start: 0.6902 (m100) cc_final: 0.6076 (m100) REVERT: H 57 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8128 (mtmt) REVERT: H 59 TYR cc_start: 0.7327 (m-80) cc_final: 0.6372 (m-80) REVERT: H 66 ARG cc_start: 0.6565 (ptt90) cc_final: 0.5790 (ptt90) REVERT: H 67 PHE cc_start: 0.8009 (m-10) cc_final: 0.6918 (m-10) REVERT: H 80 LEU cc_start: 0.7472 (pp) cc_final: 0.7184 (pp) REVERT: H 91 PHE cc_start: 0.6147 (m-80) cc_final: 0.5367 (m-80) REVERT: L 30 ASN cc_start: 0.7772 (t0) cc_final: 0.7344 (t0) REVERT: L 32 PHE cc_start: 0.7635 (m-80) cc_final: 0.7426 (m-80) REVERT: L 39 LYS cc_start: 0.7291 (mmtt) cc_final: 0.7057 (mptt) REVERT: L 49 TYR cc_start: 0.7607 (p90) cc_final: 0.6700 (p90) REVERT: L 53 ASN cc_start: 0.8491 (m-40) cc_final: 0.7782 (t0) REVERT: L 78 LEU cc_start: 0.7685 (tt) cc_final: 0.7275 (mt) REVERT: L 83 ILE cc_start: 0.8306 (mt) cc_final: 0.7964 (mt) REVERT: L 87 TYR cc_start: 0.6851 (m-80) cc_final: 0.6132 (m-80) REVERT: M 35 TYR cc_start: 0.7885 (m-80) cc_final: 0.7658 (m-80) REVERT: M 37 ILE cc_start: 0.8825 (mt) cc_final: 0.8507 (tt) REVERT: N 87 TYR cc_start: 0.6647 (m-80) cc_final: 0.6182 (m-10) REVERT: N 91 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8083 (mt) outliers start: 44 outliers final: 29 residues processed: 513 average time/residue: 0.1278 time to fit residues: 84.5074 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 : 0.339 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 49 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN E 129 ASN H 105 GLN L 30 ASN L 70 HIS L 89 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 = 0.3770 r_free = 0.3770 target = 0.100041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.085932 restraints weight = 29866.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.088854 restraints weight = 17269.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.090858 restraints weight = 11390.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.092282 restraints weight = 8157.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.093312 restraints weight = 6197.488| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 9419 Z= 0.233 Angle : 0.846 11.817 12798 Z= 0.437 Chirality : 0.051 0.178 1399 Planarity : 0.006 0.056 1643 Dihedral : 6.822 58.720 1335 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.03 % Allowed : 23.64 % Favored : 70.33 % 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: -0.55 (0.25), residues: 1141 helix: -0.85 (0.38), residues: 153 sheet: 0.10 (0.26), residues: 391 loop : -0.45 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 83 TYR 0.019 0.002 TYR M 52 PHE 0.037 0.003 PHE L 95 TRP 0.030 0.003 TRP M 35A HIS 0.011 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 9402) covalent geometry : angle 0.84008 (12762) SS BOND : bond 0.00648 ( 15) SS BOND : angle 1.85482 ( 30) hydrogen bonds : bond 0.04486 ( 368) hydrogen bonds : angle 6.54778 ( 984) link_NAG-ASN : bond 0.00143 ( 2) link_NAG-ASN : angle 2.87852 ( 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 550 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 489 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: symmetry clash REVERT: B 118 GLN cc_start: 0.8506 (pm20) cc_final: 0.8098 (pm20) REVERT: B 133 ARG cc_start: 0.8601 (ttp-170) cc_final: 0.8324 (ttt-90) REVERT: B 135 MET cc_start: 0.8046 (tmm) cc_final: 0.7788 (tmm) REVERT: B 136 THR cc_start: 0.8782 (m) cc_final: 0.8476 (p) REVERT: C 72 GLU cc_start: 0.8161 (tp30) cc_final: 0.7583 (tp30) REVERT: C 74 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8076 (ttp80) REVERT: C 76 ILE cc_start: 0.9166 (mt) cc_final: 0.8945 (mt) REVERT: C 104 GLU cc_start: 0.8020 (tt0) cc_final: 0.7690 (tt0) REVERT: C 147 ASP cc_start: 0.8384 (m-30) cc_final: 0.8063 (m-30) REVERT: C 151 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8019 (mm-30) REVERT: D 100 VAL cc_start: 0.8643 (p) cc_final: 0.8354 (m) REVERT: D 102 ARG cc_start: 0.8288 (ttp-170) cc_final: 0.7963 (ttp-170) REVERT: D 119 GLN cc_start: 0.8416 (pt0) cc_final: 0.8194 (pt0) REVERT: D 136 ASN cc_start: 0.8013 (p0) cc_final: 0.7747 (p0) REVERT: D 143 ASP cc_start: 0.8676 (m-30) cc_final: 0.8439 (m-30) REVERT: D 151 MET cc_start: 0.7647 (mtt) cc_final: 0.7334 (mtm) REVERT: D 160 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7742 (mtm110) REVERT: D 165 ASP cc_start: 0.7052 (p0) cc_final: 0.6745 (p0) REVERT: E 23 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8348 (mm-30) REVERT: E 54 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7307 (mm-30) REVERT: E 73 ASN cc_start: 0.8076 (t0) cc_final: 0.7702 (t0) REVERT: E 92 PHE cc_start: 0.8878 (m-80) cc_final: 0.8605 (m-80) REVERT: E 121 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7422 (tm-30) REVERT: E 122 PHE cc_start: 0.8387 (p90) cc_final: 0.8057 (p90) REVERT: F 48 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6698 (mtm) REVERT: F 66 ARG cc_start: 0.8274 (mtm110) cc_final: 0.7959 (mtp180) REVERT: F 83 ARG cc_start: 0.7516 (ptp90) cc_final: 0.7213 (ptp-110) REVERT: F 91 PHE cc_start: 0.7215 (m-10) cc_final: 0.6910 (m-10) REVERT: F 100 TYR cc_start: 0.7203 (t80) cc_final: 0.6884 (t80) REVERT: F 100 MET cc_start: 0.8177 (mtm) cc_final: 0.7651 (mpp) REVERT: G 27 ARG cc_start: 0.8578 (ptt-90) cc_final: 0.8114 (ptt-90) REVERT: G 31 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8076 (mtmm) REVERT: G 54 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7371 (mtp-110) REVERT: G 60 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7838 (mt-10) REVERT: G 87 TYR cc_start: 0.8223 (m-80) cc_final: 0.8008 (m-80) REVERT: H 27 PHE cc_start: 0.7897 (p90) cc_final: 0.7403 (p90) REVERT: H 34 MET cc_start: 0.7264 (mmm) cc_final: 0.6989 (mmm) REVERT: H 36 TRP cc_start: 0.6691 (m100) cc_final: 0.5957 (m100) REVERT: H 57 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8203 (mtmt) REVERT: H 59 TYR cc_start: 0.7391 (m-80) cc_final: 0.6213 (m-80) REVERT: H 80 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7090 (pp) REVERT: H 82 MET cc_start: 0.7593 (mpp) cc_final: 0.7391 (mpp) REVERT: H 91 PHE cc_start: 0.6036 (m-80) cc_final: 0.5306 (m-80) REVERT: L 53 ASN cc_start: 0.8515 (m-40) cc_final: 0.7908 (t0) REVERT: L 78 LEU cc_start: 0.7750 (tt) cc_final: 0.7303 (mt) REVERT: L 83 ILE cc_start: 0.8261 (mt) cc_final: 0.7856 (mt) REVERT: L 87 TYR cc_start: 0.6862 (m-80) cc_final: 0.6227 (m-80) REVERT: L 92 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7461 (tm-30) REVERT: M 38 ARG cc_start: 0.7698 (ptt180) cc_final: 0.7428 (ttp-110) REVERT: M 53 HIS cc_start: 0.8230 (p-80) cc_final: 0.7787 (p-80) REVERT: M 58 PHE cc_start: 0.7933 (m-10) cc_final: 0.7634 (m-10) REVERT: M 82 ILE cc_start: 0.8374 (mp) cc_final: 0.8025 (mm) REVERT: N 75 ILE cc_start: 0.8079 (mp) cc_final: 0.7686 (mm) REVERT: N 91 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8106 (mt) outliers start: 61 outliers final: 43 residues processed: 507 average time/residue: 0.1216 time to fit residues: 79.8683 Evaluate side-chains 514 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 468 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 165 THR 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 C residue 143 ILE Chi-restraints excluded: chain D residue 69 LEU 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 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 27 LYS 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 5 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 52 ASN 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 H residue 52 LEU Chi-restraints excluded: chain H residue 80 LEU 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 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 72 THR Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 96 ASN 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: 4.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 92 optimal weight: 0.0270 chunk 109 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN E 62 ASN G 17 GLN G 37 GLN G 52 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS M 39 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.101686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.087523 restraints weight = 29786.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.090503 restraints weight = 17070.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.092521 restraints weight = 11167.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.093938 restraints weight = 7982.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.094993 restraints weight = 6051.914| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9419 Z= 0.182 Angle : 0.827 11.417 12798 Z= 0.417 Chirality : 0.051 0.205 1399 Planarity : 0.006 0.060 1643 Dihedral : 6.736 59.577 1335 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 6.53 % Allowed : 26.01 % Favored : 67.46 % 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: -0.45 (0.25), residues: 1141 helix: -0.72 (0.39), residues: 154 sheet: 0.23 (0.27), residues: 384 loop : -0.45 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 93 TYR 0.023 0.002 TYR F 27 PHE 0.018 0.003 PHE L 95 TRP 0.030 0.003 TRP F 50 HIS 0.012 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9402) covalent geometry : angle 0.82311 (12762) SS BOND : bond 0.00540 ( 15) SS BOND : angle 1.54320 ( 30) hydrogen bonds : bond 0.03996 ( 368) hydrogen bonds : angle 6.23656 ( 984) link_NAG-ASN : bond 0.00336 ( 2) link_NAG-ASN : angle 2.44264 ( 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 547 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 481 time to evaluate : 0.505 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 87 ARG cc_start: 0.6257 (mpt180) cc_final: 0.5675 (mpt180) REVERT: B 114 ASN cc_start: 0.8776 (m-40) cc_final: 0.8553 (m-40) REVERT: B 118 GLN cc_start: 0.8482 (pm20) cc_final: 0.8041 (pm20) REVERT: B 135 MET cc_start: 0.7930 (tmm) cc_final: 0.7695 (tmm) REVERT: B 157 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7485 (p0) REVERT: B 162 TYR cc_start: 0.6779 (m-80) cc_final: 0.6553 (m-80) REVERT: C 32 GLU cc_start: 0.2624 (OUTLIER) cc_final: 0.1858 (mp0) REVERT: C 72 GLU cc_start: 0.8028 (tp30) cc_final: 0.7302 (tp30) REVERT: C 76 ILE cc_start: 0.9171 (mt) cc_final: 0.8926 (mm) REVERT: C 80 MET cc_start: 0.6917 (mmt) cc_final: 0.5770 (ttt) REVERT: C 92 LYS cc_start: 0.9079 (mttp) cc_final: 0.8786 (mtmm) REVERT: C 101 LEU cc_start: 0.9064 (mm) cc_final: 0.8860 (mm) REVERT: C 104 GLU cc_start: 0.8046 (tt0) cc_final: 0.7828 (tt0) REVERT: C 120 TYR cc_start: 0.8741 (m-10) cc_final: 0.8528 (m-10) REVERT: C 122 LEU cc_start: 0.8853 (mm) cc_final: 0.8593 (mm) REVERT: C 134 ASN cc_start: 0.7886 (t0) cc_final: 0.7240 (t0) REVERT: C 135 LEU cc_start: 0.7720 (mt) cc_final: 0.6370 (mp) REVERT: C 147 ASP cc_start: 0.8310 (m-30) cc_final: 0.8082 (m-30) REVERT: D 100 VAL cc_start: 0.8716 (p) cc_final: 0.8238 (m) REVERT: D 143 ASP cc_start: 0.8608 (m-30) cc_final: 0.8400 (m-30) REVERT: D 151 MET cc_start: 0.7594 (mtt) cc_final: 0.7295 (mtt) REVERT: D 155 GLN cc_start: 0.7699 (tp40) cc_final: 0.6655 (tm-30) REVERT: D 160 ARG cc_start: 0.8114 (mtm180) cc_final: 0.7693 (mtm110) REVERT: D 165 ASP cc_start: 0.7268 (p0) cc_final: 0.6812 (p0) REVERT: D 171 MET cc_start: 0.7224 (mmm) cc_final: 0.6781 (mmm) REVERT: E 23 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8357 (mm-30) REVERT: E 54 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7269 (mm-30) REVERT: E 73 ASN cc_start: 0.8092 (t0) cc_final: 0.7760 (t0) REVERT: E 92 PHE cc_start: 0.8882 (m-10) cc_final: 0.8677 (m-80) REVERT: E 121 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7500 (tm-30) REVERT: E 122 PHE cc_start: 0.8404 (p90) cc_final: 0.8026 (p90) REVERT: F 37 VAL cc_start: 0.8289 (t) cc_final: 0.7792 (m) REVERT: F 66 ARG cc_start: 0.8232 (mtm110) cc_final: 0.7783 (mtp180) REVERT: F 100 TYR cc_start: 0.7227 (t80) cc_final: 0.6841 (t80) REVERT: F 100 MET cc_start: 0.8129 (mtm) cc_final: 0.6895 (mpp) REVERT: G 29 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6619 (m-30) REVERT: G 31 LYS cc_start: 0.8363 (mtmm) cc_final: 0.8007 (mtmm) REVERT: G 54 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7343 (mtp-110) REVERT: G 60 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8083 (mt-10) REVERT: G 69 ASN cc_start: 0.8925 (m-40) cc_final: 0.8321 (m-40) REVERT: H 27 PHE cc_start: 0.7851 (p90) cc_final: 0.7587 (p90) REVERT: H 34 MET cc_start: 0.7264 (mmm) cc_final: 0.6855 (mmm) REVERT: H 36 TRP cc_start: 0.6539 (m100) cc_final: 0.5901 (m100) REVERT: H 57 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8297 (mtmt) REVERT: H 59 TYR cc_start: 0.7461 (m-80) cc_final: 0.6199 (m-80) REVERT: H 80 LEU cc_start: 0.7188 (pp) cc_final: 0.6932 (pp) REVERT: H 91 PHE cc_start: 0.6055 (m-80) cc_final: 0.5427 (m-80) REVERT: L 30 ASN cc_start: 0.7876 (t0) cc_final: 0.7569 (t0) REVERT: L 39 LYS cc_start: 0.7521 (mptt) cc_final: 0.7310 (mptt) REVERT: L 53 ASN cc_start: 0.8462 (m-40) cc_final: 0.7861 (t0) REVERT: L 87 TYR cc_start: 0.6890 (m-80) cc_final: 0.6124 (m-80) REVERT: L 92 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7335 (tm-30) REVERT: M 47 TRP cc_start: 0.7589 (t60) cc_final: 0.6291 (t60) REVERT: M 58 PHE cc_start: 0.7990 (m-10) cc_final: 0.7713 (m-10) REVERT: M 75 LYS cc_start: 0.7489 (mtpp) cc_final: 0.6600 (ttmm) REVERT: M 80 LEU cc_start: 0.8921 (mp) cc_final: 0.8269 (mm) REVERT: M 81 LYS cc_start: 0.7917 (mppt) cc_final: 0.7264 (tttp) REVERT: N 75 ILE cc_start: 0.8029 (mp) cc_final: 0.7644 (mm) REVERT: N 91 LEU cc_start: 0.8231 (mt) cc_final: 0.7581 (mp) outliers start: 66 outliers final: 45 residues processed: 501 average time/residue: 0.1244 time to fit residues: 80.4535 Evaluate side-chains 511 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 463 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 157 ASP 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 94 THR 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 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 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 107 THR Chi-restraints excluded: chain F residue 109 VAL 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 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 L residue 1 ASP 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 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 105 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN E 62 ASN G 52 ASN L 30 ASN L 70 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.101261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.086999 restraints weight = 30223.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.089950 restraints weight = 17522.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.091984 restraints weight = 11557.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.093399 restraints weight = 8262.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.094425 restraints weight = 6289.144| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9419 Z= 0.179 Angle : 0.834 10.845 12798 Z= 0.418 Chirality : 0.051 0.290 1399 Planarity : 0.006 0.063 1643 Dihedral : 6.530 58.843 1334 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.92 % Allowed : 27.79 % Favored : 65.28 % 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: -0.53 (0.25), residues: 1141 helix: -0.68 (0.39), residues: 154 sheet: 0.18 (0.27), residues: 393 loop : -0.55 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 93 TYR 0.029 0.002 TYR C 137 PHE 0.023 0.002 PHE D 190 TRP 0.030 0.003 TRP F 50 HIS 0.011 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9402) covalent geometry : angle 0.82992 (12762) SS BOND : bond 0.00591 ( 15) SS BOND : angle 1.46853 ( 30) hydrogen bonds : bond 0.03850 ( 368) hydrogen bonds : angle 6.20096 ( 984) link_NAG-ASN : bond 0.00173 ( 2) link_NAG-ASN : angle 2.50264 ( 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 544 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 474 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLN cc_start: 0.8523 (pm20) cc_final: 0.8098 (pm20) REVERT: B 135 MET cc_start: 0.7923 (tmm) cc_final: 0.7614 (tmm) REVERT: B 157 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7532 (p0) REVERT: B 162 TYR cc_start: 0.6685 (m-80) cc_final: 0.6304 (m-80) REVERT: C 32 GLU cc_start: 0.2746 (OUTLIER) cc_final: 0.2456 (mp0) REVERT: C 72 GLU cc_start: 0.7994 (tp30) cc_final: 0.7353 (tp30) REVERT: C 76 ILE cc_start: 0.9151 (mt) cc_final: 0.8935 (mm) REVERT: C 87 GLN cc_start: 0.8596 (tp40) cc_final: 0.8307 (tp40) REVERT: C 92 LYS cc_start: 0.9046 (mttp) cc_final: 0.8775 (mtmm) REVERT: C 102 TYR cc_start: 0.8056 (t80) cc_final: 0.7004 (t80) REVERT: C 104 GLU cc_start: 0.8128 (tt0) cc_final: 0.7835 (tt0) REVERT: C 122 LEU cc_start: 0.8886 (mm) cc_final: 0.8639 (mm) REVERT: C 134 ASN cc_start: 0.7836 (t0) cc_final: 0.7300 (t0) REVERT: C 147 ASP cc_start: 0.8241 (m-30) cc_final: 0.8019 (m-30) REVERT: D 95 GLU cc_start: 0.8366 (mp0) cc_final: 0.8133 (mt-10) REVERT: D 100 VAL cc_start: 0.8696 (p) cc_final: 0.8263 (m) REVERT: D 136 ASN cc_start: 0.8034 (p0) cc_final: 0.7833 (p0) REVERT: D 143 ASP cc_start: 0.8568 (m-30) cc_final: 0.8365 (m-30) REVERT: D 151 MET cc_start: 0.7620 (mtt) cc_final: 0.7326 (mtm) REVERT: D 155 GLN cc_start: 0.7370 (tp40) cc_final: 0.6854 (tm-30) REVERT: D 160 ARG cc_start: 0.8165 (mtm180) cc_final: 0.7672 (mtm-85) REVERT: D 165 ASP cc_start: 0.7273 (p0) cc_final: 0.6850 (p0) REVERT: D 171 MET cc_start: 0.7301 (mmm) cc_final: 0.6781 (mmm) REVERT: E 23 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8254 (mm-30) REVERT: E 54 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7180 (mm-30) REVERT: E 73 ASN cc_start: 0.8037 (t0) cc_final: 0.7716 (t0) REVERT: E 74 PHE cc_start: 0.7924 (t80) cc_final: 0.7350 (t80) REVERT: E 121 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7482 (tm-30) REVERT: E 122 PHE cc_start: 0.8413 (p90) cc_final: 0.8020 (p90) REVERT: F 19 LYS cc_start: 0.7714 (tptt) cc_final: 0.7378 (tppt) REVERT: F 54 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.8015 (mmm-85) REVERT: F 66 ARG cc_start: 0.8224 (mtm110) cc_final: 0.7848 (mtp180) REVERT: F 82 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8540 (tt) REVERT: F 83 ARG cc_start: 0.7617 (ptp90) cc_final: 0.7246 (ptp-110) REVERT: F 100 TYR cc_start: 0.7234 (t80) cc_final: 0.6920 (t80) REVERT: F 100 MET cc_start: 0.8109 (mtm) cc_final: 0.6977 (mpp) REVERT: G 27 ARG cc_start: 0.8582 (ptt-90) cc_final: 0.8345 (ptt-90) REVERT: G 29 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6583 (m-30) REVERT: G 31 LYS cc_start: 0.8356 (mtmm) cc_final: 0.8048 (mtmm) REVERT: G 54 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7325 (mtp-110) REVERT: G 60 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8028 (mt-10) REVERT: H 27 PHE cc_start: 0.7857 (p90) cc_final: 0.7556 (p90) REVERT: H 34 MET cc_start: 0.7394 (mmm) cc_final: 0.6894 (mmm) REVERT: H 36 TRP cc_start: 0.6571 (m100) cc_final: 0.5927 (m100) REVERT: H 57 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8297 (mtmt) REVERT: H 59 TYR cc_start: 0.7460 (m-80) cc_final: 0.6120 (m-80) REVERT: H 91 PHE cc_start: 0.6125 (m-80) cc_final: 0.5519 (m-80) REVERT: L 30 ASN cc_start: 0.7854 (t0) cc_final: 0.7447 (t0) REVERT: L 31 GLN cc_start: 0.8290 (mp10) cc_final: 0.7981 (pm20) REVERT: L 70 HIS cc_start: 0.7607 (t70) cc_final: 0.7278 (t-90) REVERT: L 87 TYR cc_start: 0.6817 (m-80) cc_final: 0.6241 (m-80) REVERT: L 92 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7234 (tm-30) REVERT: M 47 TRP cc_start: 0.7316 (t60) cc_final: 0.5914 (t60) REVERT: M 52 TYR cc_start: 0.7420 (t80) cc_final: 0.6740 (t80) REVERT: M 58 PHE cc_start: 0.7975 (m-10) cc_final: 0.7742 (m-10) REVERT: M 75 LYS cc_start: 0.7009 (mtpp) cc_final: 0.6662 (ttpp) REVERT: M 80 LEU cc_start: 0.8963 (mp) cc_final: 0.8266 (mm) REVERT: M 81 LYS cc_start: 0.8113 (mppt) cc_final: 0.7320 (tttp) REVERT: N 39 LYS cc_start: 0.8904 (tttm) cc_final: 0.8681 (pttm) REVERT: N 75 ILE cc_start: 0.8023 (mp) cc_final: 0.7639 (mm) REVERT: N 105 ASP cc_start: 0.0325 (OUTLIER) cc_final: 0.0110 (m-30) outliers start: 70 outliers final: 48 residues processed: 494 average time/residue: 0.1199 time to fit residues: 76.6884 Evaluate side-chains 515 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 462 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU 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 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 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 143 ILE 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 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 52 ASN 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 G residue 11 VAL Chi-restraints excluded: chain G residue 29 ASP 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 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 51 ILE 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 72 THR 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: 2.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 ASN G 17 GLN G 37 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.101302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.086632 restraints weight = 29996.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.089715 restraints weight = 16972.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.091822 restraints weight = 11054.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.093283 restraints weight = 7843.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.094337 restraints weight = 5950.539| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9419 Z= 0.190 Angle : 0.862 11.144 12798 Z= 0.431 Chirality : 0.052 0.458 1399 Planarity : 0.006 0.057 1643 Dihedral : 6.582 59.057 1334 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.63 % Allowed : 28.98 % Favored : 64.39 % 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: -0.53 (0.25), residues: 1141 helix: -0.61 (0.40), residues: 154 sheet: 0.17 (0.26), residues: 401 loop : -0.57 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 108 TYR 0.057 0.003 TYR C 137 PHE 0.020 0.002 PHE L 32 TRP 0.030 0.003 TRP F 50 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9402) covalent geometry : angle 0.85662 (12762) SS BOND : bond 0.00573 ( 15) SS BOND : angle 1.89364 ( 30) hydrogen bonds : bond 0.03875 ( 368) hydrogen bonds : angle 6.18666 ( 984) link_NAG-ASN : bond 0.00132 ( 2) link_NAG-ASN : angle 2.58826 ( 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 536 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 469 time to evaluate : 0.343 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: B 99 VAL cc_start: 0.8867 (t) cc_final: 0.8546 (p) REVERT: B 118 GLN cc_start: 0.8519 (pm20) cc_final: 0.8099 (pm20) REVERT: B 135 MET cc_start: 0.7919 (tmm) cc_final: 0.7683 (tmm) REVERT: B 157 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7570 (p0) REVERT: B 162 TYR cc_start: 0.6544 (m-80) cc_final: 0.6191 (m-80) REVERT: C 32 GLU cc_start: 0.2909 (OUTLIER) cc_final: 0.2149 (mp0) REVERT: C 72 GLU cc_start: 0.8075 (tp30) cc_final: 0.7417 (tp30) REVERT: C 76 ILE cc_start: 0.9165 (mt) cc_final: 0.8953 (mm) REVERT: C 80 MET cc_start: 0.7076 (mmt) cc_final: 0.5999 (ttt) REVERT: C 87 GLN cc_start: 0.8628 (tp40) cc_final: 0.8388 (tp40) REVERT: C 104 GLU cc_start: 0.8049 (tt0) cc_final: 0.7604 (tt0) REVERT: C 122 LEU cc_start: 0.8895 (mm) cc_final: 0.8662 (mm) REVERT: D 100 VAL cc_start: 0.8803 (p) cc_final: 0.8351 (m) REVERT: D 136 ASN cc_start: 0.8022 (p0) cc_final: 0.7808 (p0) REVERT: D 143 ASP cc_start: 0.8702 (m-30) cc_final: 0.8406 (m-30) REVERT: D 151 MET cc_start: 0.7678 (mtt) cc_final: 0.7339 (mtt) REVERT: D 155 GLN cc_start: 0.7416 (tp40) cc_final: 0.6810 (tm-30) REVERT: D 160 ARG cc_start: 0.8176 (mtm180) cc_final: 0.7802 (mtm-85) REVERT: D 165 ASP cc_start: 0.7295 (p0) cc_final: 0.6860 (p0) REVERT: D 171 MET cc_start: 0.7338 (mmm) cc_final: 0.6803 (mmm) REVERT: D 177 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6319 (mm-30) REVERT: E 23 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8288 (mm-30) REVERT: E 54 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7219 (mm-30) REVERT: E 73 ASN cc_start: 0.8141 (t0) cc_final: 0.7697 (t0) REVERT: E 122 PHE cc_start: 0.8342 (p90) cc_final: 0.8057 (p90) REVERT: F 3 GLN cc_start: 0.7809 (pm20) cc_final: 0.7593 (pm20) REVERT: F 19 LYS cc_start: 0.7885 (tptt) cc_final: 0.7633 (tppt) REVERT: F 54 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.8109 (mmm-85) REVERT: F 66 ARG cc_start: 0.8305 (mtm110) cc_final: 0.7841 (mtp180) REVERT: F 82 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8540 (tt) REVERT: F 83 ARG cc_start: 0.7670 (ptp90) cc_final: 0.7254 (ptp-110) REVERT: F 96 GLU cc_start: 0.8073 (pp20) cc_final: 0.7858 (pp20) REVERT: F 100 TYR cc_start: 0.7439 (t80) cc_final: 0.6978 (t80) REVERT: F 100 MET cc_start: 0.8183 (mtm) cc_final: 0.7070 (mpp) REVERT: G 29 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: G 31 LYS cc_start: 0.8417 (mtmm) cc_final: 0.7713 (mtmm) REVERT: G 54 ARG cc_start: 0.7792 (ttp-110) cc_final: 0.7312 (mtp-110) REVERT: G 60 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8026 (mt-10) REVERT: G 83 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: H 27 PHE cc_start: 0.7986 (p90) cc_final: 0.7683 (p90) REVERT: H 34 MET cc_start: 0.7366 (mmm) cc_final: 0.7060 (mmm) REVERT: H 36 TRP cc_start: 0.6547 (m100) cc_final: 0.5851 (m100) REVERT: H 57 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8435 (mtmt) REVERT: H 59 TYR cc_start: 0.7450 (m-80) cc_final: 0.6009 (m-80) REVERT: H 91 PHE cc_start: 0.6227 (m-80) cc_final: 0.5617 (m-80) REVERT: L 4 MET cc_start: 0.6073 (mmp) cc_final: 0.5831 (mmp) REVERT: L 30 ASN cc_start: 0.7938 (t0) cc_final: 0.7613 (t0) REVERT: L 31 GLN cc_start: 0.8290 (mp10) cc_final: 0.7969 (pm20) REVERT: L 70 HIS cc_start: 0.7640 (t70) cc_final: 0.7339 (t-90) REVERT: L 87 TYR cc_start: 0.6879 (m-80) cc_final: 0.6287 (m-80) REVERT: L 92 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7051 (tm-30) REVERT: M 35 TYR cc_start: 0.7920 (m-10) cc_final: 0.7693 (m-10) REVERT: M 75 LYS cc_start: 0.6840 (mtpp) cc_final: 0.6599 (ttpp) REVERT: M 80 LEU cc_start: 0.8901 (mp) cc_final: 0.8253 (mm) REVERT: M 81 LYS cc_start: 0.7999 (mppt) cc_final: 0.7209 (tttp) REVERT: N 24 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7143 (mmm-85) REVERT: N 75 ILE cc_start: 0.8063 (mp) cc_final: 0.7697 (mm) REVERT: N 91 LEU cc_start: 0.8246 (mt) cc_final: 0.7747 (mp) outliers start: 67 outliers final: 52 residues processed: 489 average time/residue: 0.1228 time to fit residues: 77.9250 Evaluate side-chains 513 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 456 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 151 VAL 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 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 143 ILE 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 52 ASN 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 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 55 ARG 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 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 48 ILE Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN E 62 ASN L 89 GLN N 6 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.101241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.086870 restraints weight = 30427.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.089958 restraints weight = 16966.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.092049 restraints weight = 10943.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.093519 restraints weight = 7732.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.094550 restraints weight = 5835.494| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9419 Z= 0.191 Angle : 0.868 11.423 12798 Z= 0.435 Chirality : 0.052 0.425 1399 Planarity : 0.007 0.060 1643 Dihedral : 6.592 59.911 1334 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.92 % Allowed : 29.28 % 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: -0.50 (0.25), residues: 1141 helix: -0.60 (0.40), residues: 154 sheet: 0.12 (0.26), residues: 404 loop : -0.49 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 108 TYR 0.042 0.003 TYR C 137 PHE 0.030 0.002 PHE E 74 TRP 0.031 0.003 TRP F 50 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 9402) covalent geometry : angle 0.86105 (12762) SS BOND : bond 0.00495 ( 15) SS BOND : angle 2.08301 ( 30) hydrogen bonds : bond 0.03864 ( 368) hydrogen bonds : angle 6.17368 ( 984) link_NAG-ASN : bond 0.00117 ( 2) link_NAG-ASN : angle 2.62896 ( 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 540 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 470 time to evaluate : 0.269 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: 0.8796 (t) cc_final: 0.8587 (p) REVERT: B 118 GLN cc_start: 0.8495 (pm20) cc_final: 0.8091 (pm20) REVERT: B 157 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7591 (p0) REVERT: C 32 GLU cc_start: 0.2801 (OUTLIER) cc_final: 0.2071 (mp0) REVERT: C 72 GLU cc_start: 0.8046 (tp30) cc_final: 0.7751 (tp30) REVERT: C 87 GLN cc_start: 0.8618 (tp40) cc_final: 0.8363 (tp40) REVERT: C 104 GLU cc_start: 0.8023 (tt0) cc_final: 0.7586 (tt0) REVERT: C 122 LEU cc_start: 0.8892 (mm) cc_final: 0.8628 (mm) REVERT: D 56 TYR cc_start: 0.7165 (m-80) cc_final: 0.6920 (m-80) REVERT: D 90 LEU cc_start: 0.8259 (mt) cc_final: 0.8002 (mm) REVERT: D 100 VAL cc_start: 0.8831 (p) cc_final: 0.8475 (m) REVERT: D 136 ASN cc_start: 0.8051 (p0) cc_final: 0.7825 (p0) REVERT: D 143 ASP cc_start: 0.8705 (m-30) cc_final: 0.8431 (m-30) REVERT: D 151 MET cc_start: 0.7698 (mtt) cc_final: 0.7423 (mtt) REVERT: D 155 GLN cc_start: 0.7449 (tp40) cc_final: 0.6855 (tm-30) REVERT: D 160 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7749 (mtm-85) REVERT: D 165 ASP cc_start: 0.7347 (p0) cc_final: 0.7006 (p0) REVERT: D 171 MET cc_start: 0.7318 (mmm) cc_final: 0.6779 (mmm) REVERT: D 177 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6328 (mm-30) REVERT: D 209 HIS cc_start: 0.8435 (m90) cc_final: 0.8023 (m90) REVERT: E 23 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8294 (mm-30) REVERT: E 54 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7201 (mm-30) REVERT: E 73 ASN cc_start: 0.8103 (t0) cc_final: 0.7636 (t0) REVERT: E 74 PHE cc_start: 0.7459 (t80) cc_final: 0.7076 (t80) REVERT: E 78 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8506 (ttmm) REVERT: E 92 PHE cc_start: 0.8839 (m-10) cc_final: 0.8540 (m-80) REVERT: F 54 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8073 (mmm-85) REVERT: F 66 ARG cc_start: 0.8280 (mtm110) cc_final: 0.8025 (mtp180) REVERT: F 82 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8540 (tt) REVERT: F 96 GLU cc_start: 0.8118 (pp20) cc_final: 0.7823 (pp20) REVERT: F 100 TYR cc_start: 0.7495 (t80) cc_final: 0.6997 (t80) REVERT: F 100 MET cc_start: 0.8163 (mtm) cc_final: 0.7060 (mpp) REVERT: G 27 ARG cc_start: 0.8618 (ptt-90) cc_final: 0.8347 (ptt-90) REVERT: G 29 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6638 (m-30) REVERT: G 31 LYS cc_start: 0.8360 (mtmm) cc_final: 0.8120 (mtmm) REVERT: G 35 TRP cc_start: 0.8453 (m100) cc_final: 0.7172 (m100) REVERT: G 54 ARG cc_start: 0.7765 (ttp-110) cc_final: 0.7330 (mtp-110) REVERT: G 60 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8032 (mt-10) REVERT: H 27 PHE cc_start: 0.7854 (p90) cc_final: 0.7545 (p90) REVERT: H 34 MET cc_start: 0.7328 (mmm) cc_final: 0.7024 (mmm) REVERT: H 36 TRP cc_start: 0.6520 (m100) cc_final: 0.5851 (m100) REVERT: H 57 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8408 (mtmt) REVERT: H 59 TYR cc_start: 0.7525 (m-80) cc_final: 0.6071 (m-80) REVERT: H 91 PHE cc_start: 0.6138 (m-80) cc_final: 0.5529 (m-80) REVERT: L 30 ASN cc_start: 0.7949 (t0) cc_final: 0.7630 (t0) REVERT: L 70 HIS cc_start: 0.7588 (t70) cc_final: 0.7276 (t-90) REVERT: L 87 TYR cc_start: 0.6858 (m-80) cc_final: 0.6310 (m-80) REVERT: L 92 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7077 (tm-30) REVERT: L 93 ASN cc_start: 0.7353 (p0) cc_final: 0.6462 (p0) REVERT: M 51 ILE cc_start: 0.8136 (tt) cc_final: 0.7896 (tt) REVERT: M 52 TYR cc_start: 0.7549 (t80) cc_final: 0.7318 (t80) REVERT: M 80 LEU cc_start: 0.8806 (mp) cc_final: 0.8221 (mm) REVERT: M 81 LYS cc_start: 0.8093 (mppt) cc_final: 0.7290 (tttp) REVERT: N 39 LYS cc_start: 0.8952 (tttm) cc_final: 0.8740 (pttm) REVERT: N 75 ILE cc_start: 0.8049 (mp) cc_final: 0.7685 (mm) REVERT: N 91 LEU cc_start: 0.8214 (mt) cc_final: 0.7793 (mp) outliers start: 70 outliers final: 54 residues processed: 492 average time/residue: 0.1205 time to fit residues: 77.0081 Evaluate side-chains 517 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 459 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 113 LYS 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 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 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 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 29 ASP Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL 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 89 GLN Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER 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 32 TYR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 72 THR 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: 1.9990 chunk 105 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 chunk 64 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN E 62 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3798 r_free = 0.3798 target = 0.101670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.087368 restraints weight = 30244.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.090371 restraints weight = 17466.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.092394 restraints weight = 11479.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.093812 restraints weight = 8225.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.094764 restraints weight = 6268.326| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9419 Z= 0.190 Angle : 0.888 11.931 12798 Z= 0.445 Chirality : 0.053 0.380 1399 Planarity : 0.007 0.114 1643 Dihedral : 6.625 58.705 1334 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 6.92 % Allowed : 30.56 % Favored : 62.51 % 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: -0.49 (0.25), residues: 1141 helix: -0.52 (0.40), residues: 154 sheet: 0.12 (0.26), residues: 405 loop : -0.49 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 93 TYR 0.040 0.003 TYR C 137 PHE 0.041 0.003 PHE E 122 TRP 0.051 0.003 TRP G 35 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 9402) covalent geometry : angle 0.88276 (12762) SS BOND : bond 0.00519 ( 15) SS BOND : angle 1.92644 ( 30) hydrogen bonds : bond 0.03805 ( 368) hydrogen bonds : angle 6.21169 ( 984) link_NAG-ASN : bond 0.00159 ( 2) link_NAG-ASN : angle 2.53551 ( 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 536 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 466 time to evaluate : 0.319 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: B 109 LEU cc_start: 0.8726 (mm) cc_final: 0.8305 (pp) REVERT: B 118 GLN cc_start: 0.8462 (pm20) cc_final: 0.8091 (pm20) REVERT: B 157 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7631 (p0) REVERT: B 160 ARG cc_start: 0.6978 (ptm-80) cc_final: 0.6094 (ptt90) REVERT: B 162 TYR cc_start: 0.6126 (m-80) cc_final: 0.5827 (m-80) REVERT: C 32 GLU cc_start: 0.2826 (OUTLIER) cc_final: 0.1971 (mp0) REVERT: C 72 GLU cc_start: 0.7927 (tp30) cc_final: 0.7485 (tp30) REVERT: C 80 MET cc_start: 0.7274 (mmt) cc_final: 0.6130 (ttt) REVERT: C 87 GLN cc_start: 0.8545 (tp40) cc_final: 0.8303 (tp40) REVERT: C 104 GLU cc_start: 0.7965 (tt0) cc_final: 0.7591 (tt0) REVERT: C 113 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8500 (mtpp) REVERT: C 122 LEU cc_start: 0.8913 (mm) cc_final: 0.8688 (mm) REVERT: D 90 LEU cc_start: 0.8175 (mt) cc_final: 0.7899 (mm) REVERT: D 100 VAL cc_start: 0.8828 (p) cc_final: 0.8474 (m) REVERT: D 102 ARG cc_start: 0.7936 (tmm-80) cc_final: 0.7721 (ttp80) REVERT: D 143 ASP cc_start: 0.8566 (m-30) cc_final: 0.8314 (m-30) REVERT: D 155 GLN cc_start: 0.7417 (tp40) cc_final: 0.6865 (tm-30) REVERT: D 160 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7706 (mtm-85) REVERT: D 165 ASP cc_start: 0.7321 (p0) cc_final: 0.6998 (p0) REVERT: D 171 MET cc_start: 0.7228 (mmm) cc_final: 0.6686 (mmm) REVERT: D 177 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6418 (mm-30) REVERT: D 209 HIS cc_start: 0.8312 (m90) cc_final: 0.7993 (m90) REVERT: E 23 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8275 (mm-30) REVERT: E 26 GLU cc_start: 0.7992 (pt0) cc_final: 0.7522 (pt0) REVERT: E 54 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7126 (mm-30) REVERT: E 73 ASN cc_start: 0.8111 (t0) cc_final: 0.7668 (t0) REVERT: E 74 PHE cc_start: 0.7419 (t80) cc_final: 0.7185 (t80) REVERT: F 19 LYS cc_start: 0.7531 (tptt) cc_final: 0.7205 (tppt) REVERT: F 66 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7855 (mtp180) REVERT: F 82 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8624 (tt) REVERT: F 96 GLU cc_start: 0.8102 (pp20) cc_final: 0.7867 (pp20) REVERT: F 100 TYR cc_start: 0.7526 (t80) cc_final: 0.7133 (t80) REVERT: F 100 MET cc_start: 0.8114 (mtm) cc_final: 0.7126 (mpp) REVERT: G 27 ARG cc_start: 0.8598 (ptt-90) cc_final: 0.8354 (ptt-90) REVERT: G 29 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6601 (m-30) REVERT: G 37 GLN cc_start: 0.7978 (tt0) cc_final: 0.7611 (mt0) REVERT: G 53 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7752 (tptm) REVERT: G 54 ARG cc_start: 0.7700 (ttp-110) cc_final: 0.7202 (mtp-110) REVERT: G 60 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7964 (mt-10) REVERT: H 27 PHE cc_start: 0.7752 (p90) cc_final: 0.7486 (p90) REVERT: H 34 MET cc_start: 0.7194 (mmm) cc_final: 0.6951 (mmm) REVERT: H 36 TRP cc_start: 0.6429 (m100) cc_final: 0.5810 (m100) REVERT: H 57 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8496 (mtmt) REVERT: H 59 TYR cc_start: 0.7510 (m-80) cc_final: 0.6095 (m-80) REVERT: H 66 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6887 (ptm-80) REVERT: H 91 PHE cc_start: 0.6094 (m-80) cc_final: 0.5471 (m-80) REVERT: L 30 ASN cc_start: 0.7851 (t0) cc_final: 0.7595 (t0) REVERT: L 31 GLN cc_start: 0.8282 (mp10) cc_final: 0.7861 (pm20) REVERT: L 70 HIS cc_start: 0.7536 (t70) cc_final: 0.7133 (t-90) REVERT: L 87 TYR cc_start: 0.6953 (m-80) cc_final: 0.6490 (m-80) REVERT: L 92 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6947 (tm-30) REVERT: L 93 ASN cc_start: 0.7292 (p0) cc_final: 0.6408 (p0) REVERT: M 2 LEU cc_start: 0.7204 (tp) cc_final: 0.6927 (tp) REVERT: M 51 ILE cc_start: 0.8288 (tt) cc_final: 0.8071 (tt) REVERT: M 52 TYR cc_start: 0.7562 (t80) cc_final: 0.6715 (t80) REVERT: M 58 PHE cc_start: 0.8216 (m-10) cc_final: 0.7839 (m-10) REVERT: M 67 VAL cc_start: 0.8220 (m) cc_final: 0.8012 (p) REVERT: M 80 LEU cc_start: 0.8761 (mp) cc_final: 0.8193 (mm) REVERT: M 81 LYS cc_start: 0.8094 (mppt) cc_final: 0.7279 (tttp) REVERT: N 24 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7221 (ttm-80) REVERT: N 39 LYS cc_start: 0.8928 (tttm) cc_final: 0.8719 (pttm) REVERT: N 75 ILE cc_start: 0.8010 (mp) cc_final: 0.7638 (mm) REVERT: N 91 LEU cc_start: 0.8213 (mt) cc_final: 0.7800 (mp) outliers start: 70 outliers final: 58 residues processed: 487 average time/residue: 0.1194 time to fit residues: 75.6483 Evaluate side-chains 525 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 461 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 113 LYS 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 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 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 58 LYS 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 29 ASP Chi-restraints excluded: chain G residue 48 ILE 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 55 ARG 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 69 LEU 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 32 TYR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 72 THR 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: 0.8980 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN D 138 GLN E 62 ASN G 17 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.101572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.087529 restraints weight = 29933.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.090593 restraints weight = 17065.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.092718 restraints weight = 11091.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.094178 restraints weight = 7830.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.095231 restraints weight = 5882.278| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5413 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= 0.201 Angle : 0.926 11.718 12798 Z= 0.466 Chirality : 0.053 0.352 1399 Planarity : 0.007 0.109 1643 Dihedral : 6.718 59.730 1334 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 7.12 % Allowed : 30.17 % Favored : 62.71 % 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: -0.59 (0.25), residues: 1141 helix: -0.56 (0.41), residues: 152 sheet: 0.04 (0.26), residues: 400 loop : -0.56 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 93 TYR 0.037 0.003 TYR C 137 PHE 0.037 0.003 PHE E 122 TRP 0.033 0.003 TRP F 47 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9402) covalent geometry : angle 0.92105 (12762) SS BOND : bond 0.00528 ( 15) SS BOND : angle 1.99150 ( 30) hydrogen bonds : bond 0.03901 ( 368) hydrogen bonds : angle 6.33647 ( 984) link_NAG-ASN : bond 0.00170 ( 2) link_NAG-ASN : angle 2.56314 ( 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 531 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 459 time to evaluate : 0.343 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: B 118 GLN cc_start: 0.8452 (pm20) cc_final: 0.8102 (pm20) REVERT: B 157 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7703 (p0) REVERT: B 160 ARG cc_start: 0.7242 (ptm-80) cc_final: 0.6876 (ptm160) REVERT: C 72 GLU cc_start: 0.8009 (tp30) cc_final: 0.7573 (tp30) REVERT: C 74 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7636 (ttp80) REVERT: C 87 GLN cc_start: 0.8583 (tp40) cc_final: 0.8348 (tp40) REVERT: C 104 GLU cc_start: 0.8084 (tt0) cc_final: 0.7783 (tt0) REVERT: C 119 GLN cc_start: 0.8391 (tt0) cc_final: 0.8048 (tt0) REVERT: C 122 LEU cc_start: 0.8904 (mm) cc_final: 0.8629 (mm) REVERT: D 100 VAL cc_start: 0.8841 (p) cc_final: 0.8381 (m) REVERT: D 142 GLU cc_start: 0.8856 (mp0) cc_final: 0.8628 (pm20) REVERT: D 143 ASP cc_start: 0.8667 (m-30) cc_final: 0.8439 (m-30) REVERT: D 155 GLN cc_start: 0.7425 (tp40) cc_final: 0.6958 (tm-30) REVERT: D 160 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7692 (mtm-85) REVERT: D 165 ASP cc_start: 0.7333 (p0) cc_final: 0.7027 (p0) REVERT: D 171 MET cc_start: 0.7298 (mmm) cc_final: 0.6759 (mmm) REVERT: D 177 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6442 (mm-30) REVERT: D 209 HIS cc_start: 0.8377 (m90) cc_final: 0.8040 (m90) REVERT: E 23 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8253 (mm-30) REVERT: E 54 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7206 (mm-30) REVERT: E 73 ASN cc_start: 0.8189 (t0) cc_final: 0.7697 (t0) REVERT: E 74 PHE cc_start: 0.7476 (t80) cc_final: 0.7058 (t80) REVERT: E 78 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8677 (ttmt) REVERT: E 122 PHE cc_start: 0.8323 (p90) cc_final: 0.7886 (p90) REVERT: F 3 GLN cc_start: 0.7902 (pm20) cc_final: 0.7620 (pm20) REVERT: F 19 LYS cc_start: 0.7620 (tptt) cc_final: 0.7195 (tppt) REVERT: F 66 ARG cc_start: 0.8429 (mtm110) cc_final: 0.7876 (mtp180) REVERT: F 82 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8695 (tt) REVERT: F 96 GLU cc_start: 0.8165 (pp20) cc_final: 0.7902 (pp20) REVERT: F 100 TYR cc_start: 0.7557 (t80) cc_final: 0.7071 (t80) REVERT: F 100 MET cc_start: 0.8157 (mtm) cc_final: 0.7832 (mpp) REVERT: G 27 ARG cc_start: 0.8602 (ptt-90) cc_final: 0.8366 (ptt-90) REVERT: G 29 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6397 (m-30) REVERT: G 35 TRP cc_start: 0.8276 (m100) cc_final: 0.7326 (m-10) REVERT: G 53 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7817 (tptm) REVERT: G 54 ARG cc_start: 0.7598 (ttp-110) cc_final: 0.7045 (mtp-110) REVERT: G 60 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7959 (mt-10) REVERT: G 92 ASP cc_start: 0.7333 (t0) cc_final: 0.6999 (t0) REVERT: G 94 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7131 (t70) REVERT: H 27 PHE cc_start: 0.7887 (p90) cc_final: 0.7640 (p90) REVERT: H 34 MET cc_start: 0.7239 (mmm) cc_final: 0.6982 (mmm) REVERT: H 36 TRP cc_start: 0.6466 (m100) cc_final: 0.5888 (m100) REVERT: H 59 TYR cc_start: 0.7590 (m-80) cc_final: 0.6123 (m-80) REVERT: H 91 PHE cc_start: 0.6116 (m-80) cc_final: 0.5520 (m-80) REVERT: L 4 MET cc_start: 0.5909 (mmp) cc_final: 0.5568 (mmp) REVERT: L 30 ASN cc_start: 0.7893 (t0) cc_final: 0.7619 (t0) REVERT: L 31 GLN cc_start: 0.8281 (mp10) cc_final: 0.7877 (pm20) REVERT: L 87 TYR cc_start: 0.6696 (m-80) cc_final: 0.6399 (m-80) REVERT: L 92 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7043 (tm-30) REVERT: M 35 TYR cc_start: 0.7803 (m-10) cc_final: 0.7572 (m-10) REVERT: M 52 TYR cc_start: 0.7435 (t80) cc_final: 0.6793 (t80) REVERT: M 58 PHE cc_start: 0.8227 (m-10) cc_final: 0.7797 (m-10) REVERT: M 67 VAL cc_start: 0.8207 (m) cc_final: 0.7993 (p) REVERT: M 80 LEU cc_start: 0.8716 (mp) cc_final: 0.8179 (mm) REVERT: M 81 LYS cc_start: 0.8123 (mppt) cc_final: 0.7311 (tttp) REVERT: M 97 ARG cc_start: 0.6823 (ttm170) cc_final: 0.6326 (ttm170) REVERT: N 24 ARG cc_start: 0.7572 (ttm-80) cc_final: 0.7318 (ttm-80) REVERT: N 39 LYS cc_start: 0.8926 (tttm) cc_final: 0.8717 (pttm) REVERT: N 46 LEU cc_start: 0.8817 (tp) cc_final: 0.8250 (pp) REVERT: N 75 ILE cc_start: 0.8057 (mp) cc_final: 0.7692 (mm) REVERT: N 91 LEU cc_start: 0.8187 (mt) cc_final: 0.7825 (mp) outliers start: 72 outliers final: 57 residues processed: 482 average time/residue: 0.1140 time to fit residues: 71.5005 Evaluate side-chains 519 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 456 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 74 ARG 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 113 LYS 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 106 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 58 LYS 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 94 ASP 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 55 ARG 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 69 LEU 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 48 ILE Chi-restraints excluded: chain N residue 70 ASP 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 92 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 110 optimal weight: 0.0470 chunk 17 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 ASN L 70 HIS ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** 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 = 0.3822 r_free = 0.3822 target = 0.102847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.088709 restraints weight = 29889.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.091825 restraints weight = 16941.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.093935 restraints weight = 10966.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095433 restraints weight = 7750.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.096514 restraints weight = 5809.990| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9419 Z= 0.171 Angle : 0.930 11.304 12798 Z= 0.464 Chirality : 0.054 0.346 1399 Planarity : 0.007 0.126 1643 Dihedral : 6.556 57.734 1334 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.03 % Allowed : 31.95 % Favored : 62.02 % 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: -0.54 (0.25), residues: 1141 helix: -0.31 (0.42), residues: 146 sheet: 0.00 (0.26), residues: 400 loop : -0.53 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 51 TYR 0.037 0.002 TYR F 27 PHE 0.035 0.003 PHE E 122 TRP 0.040 0.003 TRP G 35 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9402) covalent geometry : angle 0.92545 (12762) SS BOND : bond 0.00493 ( 15) SS BOND : angle 1.79421 ( 30) hydrogen bonds : bond 0.03899 ( 368) hydrogen bonds : angle 6.23056 ( 984) link_NAG-ASN : bond 0.00184 ( 2) link_NAG-ASN : angle 2.38002 ( 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 523 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 462 time to evaluate : 0.342 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: B 118 GLN cc_start: 0.8507 (pm20) cc_final: 0.8123 (pm20) REVERT: B 157 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7689 (p0) REVERT: C 51 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7803 (ptt-90) REVERT: C 52 PHE cc_start: 0.8499 (m-80) cc_final: 0.8100 (m-10) REVERT: C 72 GLU cc_start: 0.7975 (tp30) cc_final: 0.7542 (tp30) REVERT: C 74 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7796 (ttp80) REVERT: C 87 GLN cc_start: 0.8578 (tp40) cc_final: 0.8367 (tp40) REVERT: C 104 GLU cc_start: 0.8025 (tt0) cc_final: 0.7629 (tt0) REVERT: C 117 LYS cc_start: 0.8519 (pttt) cc_final: 0.8219 (pttt) REVERT: C 119 GLN cc_start: 0.8589 (tt0) cc_final: 0.8317 (tt0) REVERT: C 122 LEU cc_start: 0.8897 (mm) cc_final: 0.8628 (mm) REVERT: D 100 VAL cc_start: 0.8832 (p) cc_final: 0.8394 (m) REVERT: D 142 GLU cc_start: 0.8815 (mp0) cc_final: 0.8611 (pm20) REVERT: D 143 ASP cc_start: 0.8657 (m-30) cc_final: 0.8421 (m-30) REVERT: D 155 GLN cc_start: 0.7457 (tp40) cc_final: 0.6869 (tm-30) REVERT: D 160 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7678 (mtm-85) REVERT: D 165 ASP cc_start: 0.7362 (p0) cc_final: 0.7017 (p0) REVERT: D 171 MET cc_start: 0.7247 (mmm) cc_final: 0.6710 (mmm) REVERT: D 209 HIS cc_start: 0.8339 (m90) cc_final: 0.8005 (m90) REVERT: E 23 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8225 (mm-30) REVERT: E 26 GLU cc_start: 0.8000 (pt0) cc_final: 0.7252 (mt-10) REVERT: E 54 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7158 (mm-30) REVERT: E 73 ASN cc_start: 0.8142 (t0) cc_final: 0.7700 (t0) REVERT: E 74 PHE cc_start: 0.7405 (t80) cc_final: 0.7102 (t80) REVERT: F 3 GLN cc_start: 0.7882 (pm20) cc_final: 0.7654 (pm20) REVERT: F 13 LYS cc_start: 0.1872 (mptt) cc_final: 0.1282 (mmtm) REVERT: F 36 TRP cc_start: 0.8684 (m100) cc_final: 0.8468 (m100) REVERT: F 66 ARG cc_start: 0.8391 (mtm110) cc_final: 0.7850 (mtp180) REVERT: F 82 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8685 (tt) REVERT: F 96 GLU cc_start: 0.8188 (pp20) cc_final: 0.7836 (pm20) REVERT: F 100 TYR cc_start: 0.7512 (t80) cc_final: 0.7050 (t80) REVERT: F 100 MET cc_start: 0.8070 (mtm) cc_final: 0.7071 (mpp) REVERT: G 27 ARG cc_start: 0.8541 (ptt-90) cc_final: 0.8266 (ptt-90) REVERT: G 29 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6333 (m-30) REVERT: G 53 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7833 (tptm) REVERT: G 54 ARG cc_start: 0.7611 (ttp-110) cc_final: 0.7032 (mtp-110) REVERT: G 92 ASP cc_start: 0.7202 (t0) cc_final: 0.6928 (t0) REVERT: H 27 PHE cc_start: 0.7848 (p90) cc_final: 0.7569 (p90) REVERT: H 34 MET cc_start: 0.7220 (mmm) cc_final: 0.6940 (mmm) REVERT: H 36 TRP cc_start: 0.6397 (m100) cc_final: 0.5793 (m100) REVERT: H 59 TYR cc_start: 0.7395 (m-80) cc_final: 0.6369 (m-80) REVERT: H 91 PHE cc_start: 0.6143 (m-80) cc_final: 0.5559 (m-80) REVERT: L 4 MET cc_start: 0.5899 (mmp) cc_final: 0.5612 (mmp) REVERT: L 30 ASN cc_start: 0.7900 (t0) cc_final: 0.7537 (t0) REVERT: L 31 GLN cc_start: 0.8277 (mp10) cc_final: 0.7775 (pm20) REVERT: L 36 TYR cc_start: 0.5395 (m-80) cc_final: 0.5072 (m-80) REVERT: L 70 HIS cc_start: 0.7569 (t70) cc_final: 0.7153 (t-90) REVERT: L 87 TYR cc_start: 0.6840 (m-80) cc_final: 0.6491 (m-80) REVERT: L 92 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7005 (tm-30) REVERT: M 33 ASN cc_start: 0.7961 (p0) cc_final: 0.7637 (p0) REVERT: M 39 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8133 (tp40) REVERT: M 58 PHE cc_start: 0.8255 (m-10) cc_final: 0.7900 (m-10) REVERT: M 67 VAL cc_start: 0.8207 (m) cc_final: 0.7972 (p) REVERT: M 80 LEU cc_start: 0.8677 (mp) cc_final: 0.8168 (mm) REVERT: M 81 LYS cc_start: 0.8150 (mppt) cc_final: 0.7310 (tttp) REVERT: M 94 ARG cc_start: 0.6637 (ttt-90) cc_final: 0.6090 (tmm-80) REVERT: N 24 ARG cc_start: 0.7461 (ttm-80) cc_final: 0.7166 (ttm-80) REVERT: N 46 LEU cc_start: 0.8786 (tp) cc_final: 0.8200 (pp) REVERT: N 75 ILE cc_start: 0.8043 (mp) cc_final: 0.7679 (mm) REVERT: N 91 LEU cc_start: 0.8125 (mt) cc_final: 0.7822 (mp) outliers start: 61 outliers final: 53 residues processed: 482 average time/residue: 0.1143 time to fit residues: 71.8033 Evaluate side-chains 516 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 458 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 74 ARG 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 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 146 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 112 SER Chi-restraints excluded: chain E residue 113 LEU 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 58 LYS 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 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 55 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 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 78 PHE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 70 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.102313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.088066 restraints weight = 29707.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.091151 restraints weight = 16931.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.093256 restraints weight = 11012.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.094732 restraints weight = 7800.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.095791 restraints weight = 5887.460| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 9419 Z= 0.274 Angle : 1.227 59.146 12798 Z= 0.680 Chirality : 0.059 0.898 1399 Planarity : 0.007 0.143 1643 Dihedral : 6.601 57.705 1334 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 26.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 6.33 % Allowed : 31.85 % Favored : 61.82 % Cbeta Deviations : 0.09 % 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: -0.56 (0.25), residues: 1141 helix: -0.35 (0.42), residues: 146 sheet: -0.01 (0.26), residues: 398 loop : -0.54 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 160 TYR 0.034 0.003 TYR F 27 PHE 0.034 0.003 PHE E 122 TRP 0.037 0.003 TRP G 35 HIS 0.006 0.002 HIS M 53 Details of bonding type rmsd covalent geometry : bond 0.00628 ( 9402) covalent geometry : angle 1.20559 (12762) SS BOND : bond 0.00589 ( 15) SS BOND : angle 4.79131 ( 30) hydrogen bonds : bond 0.03925 ( 368) hydrogen bonds : angle 6.24191 ( 984) link_NAG-ASN : bond 0.00160 ( 2) link_NAG-ASN : angle 2.40774 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2473.95 seconds wall clock time: 43 minutes 16.98 seconds (2596.98 seconds total)