Starting phenix.real_space_refine on Mon Jul 28 18:00:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m30_23640/07_2025/7m30_23640.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m30_23640/07_2025/7m30_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_23640/07_2025/7m30_23640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m30_23640/07_2025/7m30_23640.map" model { file = "/net/cci-nas-00/data/ceres_data/7m30_23640/07_2025/7m30_23640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m30_23640/07_2025/7m30_23640.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.21, per 1000 atoms: 0.78 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.56 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: 2.83 Time building geometry restraints manager: 3.04 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: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.390 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 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 TRP 0.035 0.003 TRP D 112 HIS 0.012 0.002 HIS F 35 PHE 0.031 0.003 PHE D 190 TYR 0.028 0.005 TYR E 65 ARG 0.067 0.010 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 2) link_NAG-ASN : angle 3.30815 ( 6) hydrogen bonds : bond 0.13648 ( 368) hydrogen bonds : angle 7.46840 ( 984) SS BOND : bond 0.00843 ( 15) SS BOND : angle 3.30662 ( 30) covalent geometry : bond 0.00538 ( 9402) covalent geometry : angle 1.15137 (12762) *********************** 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 : 1.261 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: B 89 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7600 (mpt180) REVERT: B 114 ASN cc_start: 0.8619 (m-40) cc_final: 0.8402 (m-40) REVERT: B 118 GLN cc_start: 0.8721 (pm20) cc_final: 0.8337 (pm20) REVERT: B 133 ARG cc_start: 0.8778 (ttp-170) cc_final: 0.8380 (ttt-90) REVERT: B 135 MET cc_start: 0.8752 (tmm) cc_final: 0.8319 (tmm) REVERT: C 46 PHE cc_start: 0.8842 (p90) cc_final: 0.8535 (p90) REVERT: C 72 GLU cc_start: 0.8464 (tp30) cc_final: 0.7795 (tp30) REVERT: C 76 ILE cc_start: 0.9034 (mt) cc_final: 0.8813 (mm) REVERT: C 85 THR cc_start: 0.8458 (t) cc_final: 0.8037 (m) REVERT: C 91 ASN cc_start: 0.8892 (m-40) cc_final: 0.8620 (m-40) REVERT: C 92 LYS cc_start: 0.9191 (mttm) cc_final: 0.8976 (mttp) REVERT: C 93 LEU cc_start: 0.8930 (mp) cc_final: 0.8436 (mp) REVERT: C 97 ASN cc_start: 0.8112 (m-40) cc_final: 0.7701 (m-40) REVERT: C 101 LEU cc_start: 0.8994 (mt) cc_final: 0.8670 (mt) REVERT: C 103 LEU cc_start: 0.8499 (tp) cc_final: 0.8226 (tp) REVERT: C 147 ASP cc_start: 0.8901 (m-30) cc_final: 0.8349 (m-30) REVERT: C 151 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8525 (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: 0.6842 (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: 0.8704 (m-30) REVERT: D 159 LEU cc_start: 0.8750 (tp) cc_final: 0.8359 (tp) REVERT: D 160 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7572 (mpp80) REVERT: D 161 PHE cc_start: 0.8413 (p90) cc_final: 0.7604 (p90) REVERT: D 163 VAL cc_start: 0.8582 (t) cc_final: 0.8264 (p) REVERT: D 165 ASP cc_start: 0.7672 (p0) cc_final: 0.7184 (p0) REVERT: D 171 MET cc_start: 0.7626 (mmm) cc_final: 0.7369 (mmm) REVERT: D 174 MET cc_start: 0.8301 (ttp) cc_final: 0.8073 (ttp) REVERT: D 191 GLN cc_start: 0.7826 (pt0) cc_final: 0.7574 (pt0) REVERT: D 212 LEU cc_start: 0.9012 (mm) cc_final: 0.8578 (mp) REVERT: E 23 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8513 (mm-30) REVERT: E 29 ASP cc_start: 0.8633 (p0) cc_final: 0.8409 (p0) REVERT: E 30 TYR cc_start: 0.8697 (m-80) cc_final: 0.8332 (m-80) REVERT: E 44 LEU cc_start: 0.9063 (mp) cc_final: 0.8796 (mp) REVERT: E 51 LYS cc_start: 0.9188 (tttt) cc_final: 0.8983 (tttm) REVERT: E 54 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7672 (mm-30) REVERT: E 63 TYR cc_start: 0.8742 (t80) cc_final: 0.8437 (t80) REVERT: E 71 LEU cc_start: 0.8820 (mm) cc_final: 0.8587 (mt) REVERT: E 72 ASP cc_start: 0.8647 (p0) cc_final: 0.8362 (p0) REVERT: E 73 ASN cc_start: 0.7776 (t0) cc_final: 0.7520 (t0) REVERT: E 74 PHE cc_start: 0.8368 (t80) cc_final: 0.8131 (t80) REVERT: E 78 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8535 (ttmt) REVERT: E 88 LEU cc_start: 0.9044 (tt) cc_final: 0.8705 (tt) REVERT: E 92 PHE cc_start: 0.9098 (m-80) cc_final: 0.8866 (m-80) REVERT: E 121 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7486 (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: 0.6763 (ttt-90) REVERT: F 57 THR cc_start: 0.7418 (p) cc_final: 0.7161 (p) REVERT: F 68 THR cc_start: 0.8194 (p) cc_final: 0.7925 (p) REVERT: F 69 ILE cc_start: 0.8595 (mt) cc_final: 0.8220 (mt) REVERT: F 97 SER cc_start: 0.8272 (p) cc_final: 0.7295 (p) REVERT: G 54 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.6785 (mtm110) REVERT: H 59 TYR cc_start: 0.5854 (m-80) cc_final: 0.5336 (m-80) REVERT: M 52 TYR cc_start: 0.5701 (t80) cc_final: 0.5404 (t80) REVERT: M 54 THR cc_start: 0.7213 (p) cc_final: 0.6976 (p) REVERT: M 58 PHE cc_start: 0.7560 (m-80) cc_final: 0.7252 (m-10) REVERT: M 63 PHE cc_start: 0.6046 (m-80) cc_final: 0.5631 (m-80) REVERT: M 67 VAL cc_start: 0.7199 (m) cc_final: 0.6978 (p) REVERT: M 69 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6737 (tp) REVERT: N 106 ILE cc_start: 0.3932 (pt) cc_final: 0.3496 (pt) outliers start: 9 outliers final: 4 residues processed: 550 average time/residue: 0.3351 time to fit residues: 236.6709 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 : 1.023 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.5980 chunk 84 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3821 r_free = 0.3821 target = 0.102321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.087956 restraints weight = 30117.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.091002 restraints weight = 16701.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.093117 restraints weight = 10745.094| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 9419 Z= 0.206 Angle : 0.869 13.166 12798 Z= 0.447 Chirality : 0.051 0.203 1399 Planarity : 0.006 0.058 1643 Dihedral : 6.709 59.558 1341 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.96 % Allowed : 20.18 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1141 helix: -0.90 (0.38), residues: 156 sheet: 0.13 (0.25), residues: 406 loop : -0.23 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP F 47 HIS 0.014 0.003 HIS H 35 PHE 0.030 0.003 PHE D 147 TYR 0.029 0.003 TYR D 56 ARG 0.009 0.001 ARG M 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00099 ( 2) link_NAG-ASN : angle 2.62505 ( 6) hydrogen bonds : bond 0.04914 ( 368) hydrogen bonds : angle 6.44854 ( 984) SS BOND : bond 0.00654 ( 15) SS BOND : angle 1.89232 ( 30) covalent geometry : bond 0.00465 ( 9402) covalent geometry : angle 0.86365 (12762) *********************** 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 542 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 502 time to evaluate : 1.585 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: 0.7798 (mpt180) cc_final: 0.7564 (mpt180) REVERT: B 99 VAL cc_start: 0.8591 (p) cc_final: 0.8234 (t) REVERT: B 113 TYR cc_start: 0.8366 (t80) cc_final: 0.8164 (t80) REVERT: B 118 GLN cc_start: 0.8584 (pm20) cc_final: 0.8202 (pm20) REVERT: B 133 ARG cc_start: 0.8689 (ttp-170) cc_final: 0.8426 (ttt180) REVERT: B 135 MET cc_start: 0.8295 (tmm) cc_final: 0.8007 (tmm) REVERT: B 136 THR cc_start: 0.8772 (m) cc_final: 0.8544 (p) REVERT: B 162 TYR cc_start: 0.6843 (m-80) cc_final: 0.6602 (m-80) REVERT: C 32 GLU cc_start: 0.3134 (OUTLIER) cc_final: 0.2535 (mp0) REVERT: C 44 TYR cc_start: 0.7996 (p90) cc_final: 0.7550 (p90) REVERT: C 48 MET cc_start: 0.8490 (mpp) cc_final: 0.8240 (mmp) REVERT: C 72 GLU cc_start: 0.8280 (tp30) cc_final: 0.7589 (tp30) REVERT: C 74 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8074 (ttp80) REVERT: C 76 ILE cc_start: 0.9177 (mt) cc_final: 0.8946 (mm) REVERT: C 85 THR cc_start: 0.8409 (t) cc_final: 0.7698 (m) REVERT: C 91 ASN cc_start: 0.8907 (m-40) cc_final: 0.8658 (m-40) REVERT: C 92 LYS cc_start: 0.9122 (mttm) cc_final: 0.8887 (mttp) REVERT: C 97 ASN cc_start: 0.8179 (m-40) cc_final: 0.7889 (m-40) REVERT: C 104 GLU cc_start: 0.8168 (tt0) cc_final: 0.7788 (tt0) REVERT: C 147 ASP cc_start: 0.8643 (m-30) cc_final: 0.8094 (m-30) REVERT: D 69 LEU cc_start: 0.9163 (mm) cc_final: 0.8677 (mm) REVERT: D 95 GLU cc_start: 0.8564 (tp30) cc_final: 0.8346 (mt-10) REVERT: D 99 LEU cc_start: 0.8272 (tt) cc_final: 0.7847 (pp) REVERT: D 119 GLN cc_start: 0.8458 (pt0) cc_final: 0.8221 (pt0) REVERT: D 136 ASN cc_start: 0.8126 (p0) cc_final: 0.7890 (p0) REVERT: D 143 ASP cc_start: 0.8757 (m-30) cc_final: 0.8546 (m-30) REVERT: D 151 MET cc_start: 0.7711 (mtm) cc_final: 0.7443 (mtm) REVERT: D 160 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7617 (mtm110) REVERT: D 191 GLN cc_start: 0.7874 (pt0) cc_final: 0.7623 (pt0) REVERT: D 193 ARG cc_start: 0.8441 (ptp-110) cc_final: 0.8232 (ptp-110) REVERT: D 212 LEU cc_start: 0.8897 (mm) cc_final: 0.8547 (mp) REVERT: E 23 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8344 (mm-30) REVERT: E 44 LEU cc_start: 0.8958 (mp) cc_final: 0.8758 (mp) REVERT: E 51 LYS cc_start: 0.9146 (tttt) cc_final: 0.8932 (tttm) REVERT: E 54 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7325 (mm-30) REVERT: E 71 LEU cc_start: 0.8837 (mm) cc_final: 0.8628 (mt) REVERT: E 72 ASP cc_start: 0.8347 (p0) cc_final: 0.8141 (p0) REVERT: E 73 ASN cc_start: 0.8000 (t0) cc_final: 0.7769 (t0) REVERT: E 121 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7514 (tm-30) REVERT: E 122 PHE cc_start: 0.8333 (p90) cc_final: 0.7956 (p90) REVERT: E 125 ARG cc_start: 0.7327 (ttm-80) cc_final: 0.6478 (ttt-90) REVERT: F 37 VAL cc_start: 0.8323 (t) cc_final: 0.7863 (m) REVERT: F 66 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8021 (mtp180) REVERT: F 91 PHE cc_start: 0.7466 (m-10) cc_final: 0.7197 (m-10) REVERT: F 100 TYR cc_start: 0.7229 (t80) cc_final: 0.6860 (t80) REVERT: G 27 ARG cc_start: 0.8404 (ptt-90) cc_final: 0.7957 (ptt-90) REVERT: G 31 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8028 (mtmm) REVERT: G 37 GLN cc_start: 0.7624 (tt0) cc_final: 0.7381 (tt0) REVERT: G 54 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.7261 (mtp-110) REVERT: G 60 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7917 (mt-10) REVERT: G 105 THR cc_start: 0.5610 (p) cc_final: 0.4917 (p) REVERT: H 27 PHE cc_start: 0.7836 (p90) cc_final: 0.7419 (p90) REVERT: H 36 TRP cc_start: 0.6867 (m100) cc_final: 0.6019 (m100) REVERT: H 57 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8145 (mttt) REVERT: H 59 TYR cc_start: 0.7327 (m-80) cc_final: 0.6400 (m-80) REVERT: H 66 ARG cc_start: 0.6671 (ptt90) cc_final: 0.5855 (ptt90) REVERT: H 67 PHE cc_start: 0.8055 (m-10) cc_final: 0.6936 (m-10) REVERT: H 80 LEU cc_start: 0.7590 (pp) cc_final: 0.7258 (pp) REVERT: H 91 PHE cc_start: 0.6241 (m-80) cc_final: 0.5421 (m-80) REVERT: L 30 ASN cc_start: 0.7814 (t0) cc_final: 0.7358 (t0) REVERT: L 49 TYR cc_start: 0.7631 (p90) cc_final: 0.6777 (p90) REVERT: L 53 ASN cc_start: 0.8458 (m-40) cc_final: 0.7727 (t0) REVERT: L 78 LEU cc_start: 0.7714 (tt) cc_final: 0.7283 (mt) REVERT: L 83 ILE cc_start: 0.8288 (mt) cc_final: 0.7944 (mt) REVERT: L 87 TYR cc_start: 0.6786 (m-80) cc_final: 0.6111 (m-80) REVERT: N 87 TYR cc_start: 0.6695 (m-80) cc_final: 0.6276 (m-10) REVERT: N 91 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8143 (mt) outliers start: 40 outliers final: 27 residues processed: 512 average time/residue: 0.3106 time to fit residues: 206.1851 Evaluate side-chains 511 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 482 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 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 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 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 89 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 G 89 GLN H 105 GLN L 30 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.101533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.087368 restraints weight = 29957.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.090359 restraints weight = 17251.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.092434 restraints weight = 11321.947| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9419 Z= 0.193 Angle : 0.821 11.468 12798 Z= 0.422 Chirality : 0.050 0.168 1399 Planarity : 0.006 0.047 1643 Dihedral : 6.553 58.860 1335 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.95 % Allowed : 24.23 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1141 helix: -0.83 (0.38), residues: 155 sheet: 0.14 (0.25), residues: 403 loop : -0.37 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP M 35A HIS 0.010 0.002 HIS H 35 PHE 0.021 0.002 PHE D 190 TYR 0.019 0.002 TYR L 91 ARG 0.012 0.001 ARG M 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 2) link_NAG-ASN : angle 2.56343 ( 6) hydrogen bonds : bond 0.04409 ( 368) hydrogen bonds : angle 6.28655 ( 984) SS BOND : bond 0.00588 ( 15) SS BOND : angle 1.69194 ( 30) covalent geometry : bond 0.00439 ( 9402) covalent geometry : angle 0.81662 (12762) *********************** 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 544 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 494 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASN cc_start: 0.8716 (m-40) cc_final: 0.8509 (m-40) REVERT: B 118 GLN cc_start: 0.8497 (pm20) cc_final: 0.8057 (pm20) REVERT: B 135 MET cc_start: 0.8062 (tmm) cc_final: 0.7819 (tmm) REVERT: B 136 THR cc_start: 0.8785 (m) cc_final: 0.8499 (p) REVERT: C 72 GLU cc_start: 0.8201 (tp30) cc_final: 0.7417 (tp30) REVERT: C 74 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8142 (ttp80) REVERT: C 76 ILE cc_start: 0.9138 (mt) cc_final: 0.8849 (mm) REVERT: C 97 ASN cc_start: 0.8109 (m-40) cc_final: 0.7780 (m-40) REVERT: C 104 GLU cc_start: 0.8015 (tt0) cc_final: 0.7748 (tt0) REVERT: C 147 ASP cc_start: 0.8348 (m-30) cc_final: 0.7992 (m-30) REVERT: C 151 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8047 (mm-30) REVERT: D 100 VAL cc_start: 0.8629 (p) cc_final: 0.8346 (m) REVERT: D 136 ASN cc_start: 0.8064 (p0) cc_final: 0.7797 (p0) REVERT: D 143 ASP cc_start: 0.8658 (m-30) cc_final: 0.8429 (m-30) REVERT: D 151 MET cc_start: 0.7636 (mtt) cc_final: 0.7400 (mtm) REVERT: D 155 GLN cc_start: 0.7653 (tp40) cc_final: 0.7044 (tm-30) REVERT: D 160 ARG cc_start: 0.8147 (mtm180) cc_final: 0.7718 (mtm110) REVERT: D 165 ASP cc_start: 0.7063 (p0) cc_final: 0.6742 (p0) REVERT: E 23 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8374 (mm-30) REVERT: E 54 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7327 (mm-30) REVERT: E 71 LEU cc_start: 0.8860 (mm) cc_final: 0.8660 (mt) REVERT: E 73 ASN cc_start: 0.8007 (t0) cc_final: 0.7750 (t0) REVERT: E 92 PHE cc_start: 0.8901 (m-80) cc_final: 0.8642 (m-80) REVERT: E 121 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7504 (tm-30) REVERT: E 122 PHE cc_start: 0.8408 (p90) cc_final: 0.8018 (p90) REVERT: E 125 ARG cc_start: 0.7362 (ttm-80) cc_final: 0.6477 (ttt-90) REVERT: F 37 VAL cc_start: 0.8295 (t) cc_final: 0.7833 (m) REVERT: F 48 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6833 (mtm) REVERT: F 59 TYR cc_start: 0.7520 (m-80) cc_final: 0.7199 (m-80) REVERT: F 66 ARG cc_start: 0.8426 (mtm110) cc_final: 0.7957 (mtp180) REVERT: F 100 TYR cc_start: 0.7176 (t80) cc_final: 0.6906 (t80) REVERT: F 100 MET cc_start: 0.8164 (mtm) cc_final: 0.7710 (mpp) REVERT: G 31 LYS cc_start: 0.8328 (mtmm) cc_final: 0.7984 (mtmm) REVERT: G 54 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7318 (mtp-110) REVERT: G 60 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8176 (mt-10) REVERT: G 87 TYR cc_start: 0.8199 (m-80) cc_final: 0.7991 (m-80) REVERT: H 27 PHE cc_start: 0.7780 (p90) cc_final: 0.7265 (p90) REVERT: H 34 MET cc_start: 0.7293 (mmm) cc_final: 0.7012 (mmm) REVERT: H 36 TRP cc_start: 0.6618 (m100) cc_final: 0.6002 (m100) REVERT: H 55 ARG cc_start: 0.7922 (mpp80) cc_final: 0.7647 (mpp80) REVERT: H 57 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8163 (mttt) REVERT: H 59 TYR cc_start: 0.7417 (m-80) cc_final: 0.6324 (m-80) REVERT: H 67 PHE cc_start: 0.7863 (m-10) cc_final: 0.7474 (m-10) REVERT: H 80 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7265 (pp) REVERT: H 91 PHE cc_start: 0.6126 (m-80) cc_final: 0.5397 (m-80) REVERT: L 75 ILE cc_start: 0.8066 (mp) cc_final: 0.7827 (mp) REVERT: L 78 LEU cc_start: 0.7749 (tt) cc_final: 0.7286 (mt) REVERT: L 87 TYR cc_start: 0.6793 (m-80) cc_final: 0.6211 (m-80) REVERT: L 92 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7289 (tm-30) REVERT: M 37 ILE cc_start: 0.8702 (mt) cc_final: 0.8378 (tt) REVERT: M 39 GLN cc_start: 0.8264 (tp40) cc_final: 0.7967 (tp-100) REVERT: M 53 HIS cc_start: 0.8214 (p-80) cc_final: 0.7819 (p-80) REVERT: M 58 PHE cc_start: 0.7916 (m-10) cc_final: 0.7687 (m-10) REVERT: M 72 ASP cc_start: 0.6706 (t0) cc_final: 0.6415 (t70) REVERT: M 80 LEU cc_start: 0.8560 (tp) cc_final: 0.8279 (mp) REVERT: N 24 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7483 (tpp80) REVERT: N 39 LYS cc_start: 0.8912 (tttm) cc_final: 0.8694 (pttm) REVERT: N 75 ILE cc_start: 0.8056 (mp) cc_final: 0.7646 (mm) REVERT: N 91 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7804 (mp) REVERT: N 98 PHE cc_start: 0.8478 (m-80) cc_final: 0.8250 (m-10) outliers start: 50 outliers final: 35 residues processed: 509 average time/residue: 0.3299 time to fit residues: 216.1155 Evaluate side-chains 511 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 473 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 37 GLN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.102299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.087667 restraints weight = 29590.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.090709 restraints weight = 16790.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.092823 restraints weight = 10972.859| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9419 Z= 0.171 Angle : 0.812 10.399 12798 Z= 0.410 Chirality : 0.050 0.174 1399 Planarity : 0.006 0.052 1643 Dihedral : 6.526 59.654 1335 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.43 % Allowed : 25.82 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1141 helix: -0.58 (0.39), residues: 149 sheet: 0.32 (0.27), residues: 380 loop : -0.40 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 50 HIS 0.007 0.002 HIS E 69 PHE 0.015 0.002 PHE E 74 TYR 0.023 0.002 TYR F 27 ARG 0.013 0.001 ARG F 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 2) link_NAG-ASN : angle 2.30024 ( 6) hydrogen bonds : bond 0.03985 ( 368) hydrogen bonds : angle 6.10978 ( 984) SS BOND : bond 0.00661 ( 15) SS BOND : angle 1.54481 ( 30) covalent geometry : bond 0.00393 ( 9402) covalent geometry : angle 0.80852 (12762) *********************** 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 556 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 491 time to evaluate : 1.221 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: 0.8518 (pm20) cc_final: 0.8061 (pm20) REVERT: B 135 MET cc_start: 0.8048 (tmm) cc_final: 0.7773 (tmm) REVERT: B 136 THR cc_start: 0.8655 (m) cc_final: 0.8121 (p) REVERT: C 32 GLU cc_start: 0.2725 (OUTLIER) cc_final: 0.2310 (mp0) REVERT: C 72 GLU cc_start: 0.8132 (tp30) cc_final: 0.7411 (tp30) REVERT: C 76 ILE cc_start: 0.9140 (mt) cc_final: 0.8903 (mm) REVERT: C 80 MET cc_start: 0.7023 (mmt) cc_final: 0.5849 (ttt) REVERT: C 97 ASN cc_start: 0.8036 (m-40) cc_final: 0.7809 (m-40) REVERT: C 104 GLU cc_start: 0.8051 (tt0) cc_final: 0.7588 (tt0) REVERT: C 108 ARG cc_start: 0.8465 (ttm110) cc_final: 0.8225 (ttm110) REVERT: C 120 TYR cc_start: 0.8755 (m-10) cc_final: 0.8536 (m-10) REVERT: C 121 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8772 (mm) REVERT: C 134 ASN cc_start: 0.7935 (t0) cc_final: 0.7341 (t0) REVERT: C 135 LEU cc_start: 0.7714 (mt) cc_final: 0.6603 (mp) REVERT: C 147 ASP cc_start: 0.8414 (m-30) cc_final: 0.8038 (m-30) REVERT: C 151 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8112 (mm-30) REVERT: D 89 TYR cc_start: 0.7287 (m-80) cc_final: 0.6538 (m-80) REVERT: D 100 VAL cc_start: 0.8650 (p) cc_final: 0.8243 (m) REVERT: D 101 GLU cc_start: 0.6060 (pp20) cc_final: 0.5455 (pp20) REVERT: D 143 ASP cc_start: 0.8728 (m-30) cc_final: 0.8524 (m-30) REVERT: D 151 MET cc_start: 0.7744 (mtt) cc_final: 0.7452 (mtm) REVERT: D 155 GLN cc_start: 0.7541 (tp40) cc_final: 0.6653 (tm-30) REVERT: D 160 ARG cc_start: 0.8168 (mtm180) cc_final: 0.7672 (mtm110) REVERT: D 165 ASP cc_start: 0.7339 (p0) cc_final: 0.6850 (p0) REVERT: D 198 GLU cc_start: 0.7539 (tp30) cc_final: 0.7329 (tp30) REVERT: E 23 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8436 (mm-30) REVERT: E 54 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7262 (mm-30) REVERT: E 73 ASN cc_start: 0.8079 (t0) cc_final: 0.7758 (t0) REVERT: E 92 PHE cc_start: 0.8964 (m-10) cc_final: 0.8752 (m-80) REVERT: E 121 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7470 (tm-30) REVERT: E 122 PHE cc_start: 0.8432 (p90) cc_final: 0.8037 (p90) REVERT: F 36 TRP cc_start: 0.8779 (m100) cc_final: 0.8512 (m100) REVERT: F 37 VAL cc_start: 0.8276 (t) cc_final: 0.7814 (m) REVERT: F 59 TYR cc_start: 0.7807 (m-80) cc_final: 0.7231 (m-10) REVERT: F 66 ARG cc_start: 0.8510 (mtm110) cc_final: 0.7914 (mtp180) REVERT: F 83 ARG cc_start: 0.7673 (ptp90) cc_final: 0.7459 (ptp90) REVERT: F 100 TYR cc_start: 0.7217 (t80) cc_final: 0.6841 (t80) REVERT: F 100 MET cc_start: 0.8212 (mtm) cc_final: 0.7702 (mpp) REVERT: G 27 ARG cc_start: 0.8533 (ptt-90) cc_final: 0.8005 (ptt-90) REVERT: G 29 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6695 (m-30) REVERT: G 31 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7834 (mtmm) REVERT: G 54 ARG cc_start: 0.7823 (ttp-110) cc_final: 0.7358 (mtp-110) REVERT: G 60 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7890 (mt-10) REVERT: G 69 ASN cc_start: 0.8879 (m-40) cc_final: 0.8100 (m-40) REVERT: G 89 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7463 (tp40) REVERT: H 27 PHE cc_start: 0.7880 (p90) cc_final: 0.7538 (p90) REVERT: H 34 MET cc_start: 0.7305 (mmm) cc_final: 0.6869 (mmm) REVERT: H 36 TRP cc_start: 0.6664 (m100) cc_final: 0.5896 (m100) REVERT: H 55 ARG cc_start: 0.8097 (mpp80) cc_final: 0.7729 (mpp80) REVERT: H 57 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8156 (mtmt) REVERT: H 59 TYR cc_start: 0.7443 (m-80) cc_final: 0.6239 (m-80) REVERT: H 67 PHE cc_start: 0.7950 (m-10) cc_final: 0.7603 (m-10) REVERT: H 80 LEU cc_start: 0.7490 (pp) cc_final: 0.7176 (pp) REVERT: H 91 PHE cc_start: 0.6202 (m-80) cc_final: 0.5531 (m-80) REVERT: L 4 MET cc_start: 0.7177 (mmm) cc_final: 0.6676 (mmm) REVERT: L 30 ASN cc_start: 0.7975 (t0) cc_final: 0.7721 (t0) REVERT: L 87 TYR cc_start: 0.6806 (m-80) cc_final: 0.6083 (m-80) REVERT: M 39 GLN cc_start: 0.8250 (tp40) cc_final: 0.8037 (tp-100) REVERT: M 47 TRP cc_start: 0.7747 (t60) cc_final: 0.6370 (t60) REVERT: M 53 HIS cc_start: 0.8320 (p-80) cc_final: 0.7816 (p-80) REVERT: M 58 PHE cc_start: 0.7968 (m-10) cc_final: 0.7727 (m-10) REVERT: M 80 LEU cc_start: 0.8681 (tp) cc_final: 0.8416 (mp) REVERT: N 24 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7682 (ttm-80) REVERT: N 75 ILE cc_start: 0.8093 (mp) cc_final: 0.7671 (mm) REVERT: N 87 TYR cc_start: 0.6646 (m-10) cc_final: 0.6440 (m-10) outliers start: 65 outliers final: 48 residues processed: 508 average time/residue: 0.2676 time to fit residues: 175.3608 Evaluate side-chains 523 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 472 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 LEU 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 D residue 69 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 24 THR 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 111 VAL Chi-restraints excluded: chain G residue 11 VAL 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 48 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 72 THR Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 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 105 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 0.0060 chunk 97 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.102311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.087691 restraints weight = 29932.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.090748 restraints weight = 17066.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.092812 restraints weight = 11158.458| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9419 Z= 0.167 Angle : 0.812 11.366 12798 Z= 0.408 Chirality : 0.050 0.188 1399 Planarity : 0.006 0.065 1643 Dihedral : 6.286 59.653 1334 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 6.92 % Allowed : 26.41 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1141 helix: -0.53 (0.39), residues: 149 sheet: 0.23 (0.27), residues: 385 loop : -0.42 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP G 35 HIS 0.006 0.001 HIS E 69 PHE 0.017 0.002 PHE E 74 TYR 0.026 0.002 TYR F 27 ARG 0.011 0.001 ARG E 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 2) link_NAG-ASN : angle 2.22657 ( 6) hydrogen bonds : bond 0.03792 ( 368) hydrogen bonds : angle 5.99560 ( 984) SS BOND : bond 0.00599 ( 15) SS BOND : angle 1.33715 ( 30) covalent geometry : bond 0.00389 ( 9402) covalent geometry : angle 0.80908 (12762) *********************** 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 555 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 485 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASN cc_start: 0.8881 (m-40) cc_final: 0.8586 (m-40) REVERT: B 118 GLN cc_start: 0.8539 (pm20) cc_final: 0.8086 (pm20) REVERT: B 157 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7501 (p0) REVERT: B 162 TYR cc_start: 0.6635 (m-80) cc_final: 0.6266 (m-80) REVERT: C 32 GLU cc_start: 0.2963 (OUTLIER) cc_final: 0.2133 (mp0) REVERT: C 72 GLU cc_start: 0.8094 (tp30) cc_final: 0.7423 (tp30) REVERT: C 76 ILE cc_start: 0.9145 (mt) cc_final: 0.8933 (mm) REVERT: C 104 GLU cc_start: 0.7996 (tt0) cc_final: 0.7485 (tt0) REVERT: C 121 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8773 (mm) REVERT: C 134 ASN cc_start: 0.7911 (t0) cc_final: 0.7432 (t0) REVERT: C 147 ASP cc_start: 0.8385 (m-30) cc_final: 0.8171 (m-30) REVERT: D 89 TYR cc_start: 0.7377 (m-80) cc_final: 0.6541 (m-80) REVERT: D 100 VAL cc_start: 0.8653 (p) cc_final: 0.8246 (m) REVERT: D 101 GLU cc_start: 0.6108 (pp20) cc_final: 0.5525 (pp20) REVERT: D 119 GLN cc_start: 0.8567 (pt0) cc_final: 0.7892 (pm20) REVERT: D 143 ASP cc_start: 0.8697 (m-30) cc_final: 0.8413 (m-30) REVERT: D 151 MET cc_start: 0.7708 (mtt) cc_final: 0.7464 (mtt) REVERT: D 155 GLN cc_start: 0.7442 (tp40) cc_final: 0.6709 (tm-30) REVERT: D 160 ARG cc_start: 0.8176 (mtm180) cc_final: 0.7589 (mtm-85) REVERT: D 161 PHE cc_start: 0.8293 (p90) cc_final: 0.7932 (p90) REVERT: D 165 ASP cc_start: 0.7329 (p0) cc_final: 0.6836 (p0) REVERT: D 177 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6406 (mm-30) REVERT: E 23 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8434 (mm-30) REVERT: E 54 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7231 (mm-30) REVERT: E 63 TYR cc_start: 0.8550 (t80) cc_final: 0.8329 (t80) REVERT: E 73 ASN cc_start: 0.8076 (t0) cc_final: 0.7723 (t0) REVERT: E 74 PHE cc_start: 0.8011 (t80) cc_final: 0.7490 (t80) REVERT: E 121 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7479 (tm-30) REVERT: E 122 PHE cc_start: 0.8434 (p90) cc_final: 0.8046 (p90) REVERT: F 37 VAL cc_start: 0.8280 (t) cc_final: 0.7873 (m) REVERT: F 48 MET cc_start: 0.7404 (mtm) cc_final: 0.6893 (mtt) REVERT: F 54 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8087 (mmm-85) REVERT: F 59 TYR cc_start: 0.7816 (m-80) cc_final: 0.7160 (m-10) REVERT: F 66 ARG cc_start: 0.8482 (mtm110) cc_final: 0.7895 (mtp180) REVERT: F 83 ARG cc_start: 0.7732 (ptp90) cc_final: 0.7423 (ptp90) REVERT: F 96 GLU cc_start: 0.8098 (pp20) cc_final: 0.7879 (pp20) REVERT: F 100 TYR cc_start: 0.7219 (t80) cc_final: 0.6896 (t80) REVERT: F 100 MET cc_start: 0.8177 (mtm) cc_final: 0.7711 (mpp) REVERT: G 29 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6642 (m-30) REVERT: G 31 LYS cc_start: 0.8298 (mtmm) cc_final: 0.7956 (mtmm) REVERT: G 35 TRP cc_start: 0.7834 (m100) cc_final: 0.7051 (m100) REVERT: G 37 GLN cc_start: 0.7770 (tt0) cc_final: 0.7555 (tt0) REVERT: G 53 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7826 (tptm) REVERT: G 60 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7882 (mm-30) REVERT: G 69 ASN cc_start: 0.8890 (m-40) cc_final: 0.8205 (m-40) REVERT: G 87 TYR cc_start: 0.8074 (m-80) cc_final: 0.7836 (m-80) REVERT: H 27 PHE cc_start: 0.7877 (p90) cc_final: 0.7545 (p90) REVERT: H 34 MET cc_start: 0.7272 (mmm) cc_final: 0.6810 (mmm) REVERT: H 36 TRP cc_start: 0.6552 (m100) cc_final: 0.5912 (m100) REVERT: H 57 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8223 (mtmt) REVERT: H 59 TYR cc_start: 0.7490 (m-80) cc_final: 0.6207 (m-80) REVERT: H 80 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7151 (pp) REVERT: H 91 PHE cc_start: 0.6254 (m-80) cc_final: 0.5638 (m-80) REVERT: L 4 MET cc_start: 0.7277 (mmm) cc_final: 0.6519 (mmm) REVERT: L 31 GLN cc_start: 0.8390 (mp10) cc_final: 0.7987 (pm20) REVERT: L 53 ASN cc_start: 0.8562 (m110) cc_final: 0.7930 (t0) REVERT: L 70 HIS cc_start: 0.7681 (t70) cc_final: 0.7349 (t-90) REVERT: L 78 LEU cc_start: 0.7791 (tt) cc_final: 0.7359 (mt) REVERT: L 87 TYR cc_start: 0.6783 (m-80) cc_final: 0.6138 (m-80) REVERT: M 38 ARG cc_start: 0.7786 (ptt180) cc_final: 0.7105 (ttp-170) REVERT: M 47 TRP cc_start: 0.7662 (t60) cc_final: 0.6672 (t60) REVERT: M 75 LYS cc_start: 0.7539 (mtpp) cc_final: 0.7031 (mtmm) REVERT: M 80 LEU cc_start: 0.8533 (tp) cc_final: 0.8305 (mp) REVERT: N 39 LYS cc_start: 0.8960 (tttm) cc_final: 0.8743 (pttm) REVERT: N 75 ILE cc_start: 0.8092 (mp) cc_final: 0.7685 (mm) REVERT: N 87 TYR cc_start: 0.6657 (m-10) cc_final: 0.6247 (m-10) REVERT: N 91 LEU cc_start: 0.8269 (mt) cc_final: 0.7908 (mp) REVERT: N 105 ASP cc_start: 0.0588 (OUTLIER) cc_final: 0.0147 (m-30) outliers start: 70 outliers final: 50 residues processed: 503 average time/residue: 0.3046 time to fit residues: 198.8500 Evaluate side-chains 527 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 470 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 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 121 LEU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 76 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 24 THR 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 F residue 20 VAL 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 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 48 VAL 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 72 THR Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 94 LEU 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 60 ASN Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 94 ARG 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 103 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN G 17 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.102826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.088745 restraints weight = 29846.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.091738 restraints weight = 17274.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.093775 restraints weight = 11342.031| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9419 Z= 0.160 Angle : 0.826 11.204 12798 Z= 0.413 Chirality : 0.049 0.176 1399 Planarity : 0.006 0.058 1643 Dihedral : 6.230 57.372 1334 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.53 % Allowed : 29.57 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1141 helix: -0.40 (0.40), residues: 148 sheet: 0.24 (0.27), residues: 393 loop : -0.43 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP G 35 HIS 0.006 0.001 HIS L 70 PHE 0.018 0.002 PHE E 74 TYR 0.055 0.002 TYR C 137 ARG 0.013 0.001 ARG E 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 2) link_NAG-ASN : angle 2.12043 ( 6) hydrogen bonds : bond 0.03653 ( 368) hydrogen bonds : angle 5.87796 ( 984) SS BOND : bond 0.00499 ( 15) SS BOND : angle 1.35583 ( 30) covalent geometry : bond 0.00374 ( 9402) covalent geometry : angle 0.82327 (12762) *********************** 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 537 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 471 time to evaluate : 1.052 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 118 GLN cc_start: 0.8518 (pm20) cc_final: 0.8123 (pm20) REVERT: B 157 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7548 (p0) REVERT: C 32 GLU cc_start: 0.2871 (OUTLIER) cc_final: 0.2226 (mp0) REVERT: C 48 MET cc_start: 0.8055 (mmp) cc_final: 0.7815 (mmp) REVERT: C 72 GLU cc_start: 0.8038 (tp30) cc_final: 0.7416 (tp30) REVERT: C 80 MET cc_start: 0.6977 (mmt) cc_final: 0.5924 (ttt) REVERT: C 104 GLU cc_start: 0.7936 (tt0) cc_final: 0.7452 (tt0) REVERT: C 147 ASP cc_start: 0.8200 (m-30) cc_final: 0.7662 (m-30) REVERT: D 89 TYR cc_start: 0.7375 (m-80) cc_final: 0.6517 (m-80) REVERT: D 99 LEU cc_start: 0.8236 (tt) cc_final: 0.7914 (pp) REVERT: D 101 GLU cc_start: 0.5982 (pp20) cc_final: 0.5554 (pp20) REVERT: D 119 GLN cc_start: 0.8536 (pt0) cc_final: 0.7910 (pm20) REVERT: D 143 ASP cc_start: 0.8621 (m-30) cc_final: 0.8282 (m-30) REVERT: D 151 MET cc_start: 0.7635 (mtt) cc_final: 0.7352 (mtm) REVERT: D 155 GLN cc_start: 0.7414 (tp40) cc_final: 0.6824 (tm-30) REVERT: D 160 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7848 (mtm-85) REVERT: D 165 ASP cc_start: 0.7345 (p0) cc_final: 0.6914 (p0) REVERT: D 171 MET cc_start: 0.7122 (mmm) cc_final: 0.6548 (mmm) REVERT: D 212 LEU cc_start: 0.8891 (mm) cc_final: 0.8562 (mp) REVERT: E 23 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8416 (mm-30) REVERT: E 54 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7169 (mm-30) REVERT: E 63 TYR cc_start: 0.8433 (t80) cc_final: 0.8204 (t80) REVERT: E 73 ASN cc_start: 0.8026 (t0) cc_final: 0.7593 (t0) REVERT: E 74 PHE cc_start: 0.7427 (t80) cc_final: 0.7220 (t80) REVERT: E 92 PHE cc_start: 0.8790 (m-10) cc_final: 0.8454 (m-80) REVERT: E 121 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7507 (tm-30) REVERT: E 122 PHE cc_start: 0.8398 (p90) cc_final: 0.8008 (p90) REVERT: F 54 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7905 (mmm-85) REVERT: F 66 ARG cc_start: 0.8436 (mtm110) cc_final: 0.7861 (mtp180) REVERT: F 83 ARG cc_start: 0.7686 (ptp90) cc_final: 0.7357 (ptp90) REVERT: F 100 TYR cc_start: 0.7255 (t80) cc_final: 0.6961 (t80) REVERT: F 100 MET cc_start: 0.8166 (mtm) cc_final: 0.7773 (mpp) REVERT: G 27 ARG cc_start: 0.8577 (ptt-90) cc_final: 0.8327 (ptt-90) REVERT: G 29 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6621 (m-30) REVERT: G 31 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8016 (mtmm) REVERT: G 53 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7910 (tptm) REVERT: G 54 ARG cc_start: 0.7566 (ttp-110) cc_final: 0.7197 (mtp-110) REVERT: G 60 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8015 (mt-10) REVERT: G 83 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: H 27 PHE cc_start: 0.7866 (p90) cc_final: 0.7524 (p90) REVERT: H 34 MET cc_start: 0.7050 (mmm) cc_final: 0.6804 (mmm) REVERT: H 36 TRP cc_start: 0.6460 (m100) cc_final: 0.5861 (m100) REVERT: H 57 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8305 (mttt) REVERT: H 59 TYR cc_start: 0.7433 (m-80) cc_final: 0.6216 (m-80) REVERT: H 91 PHE cc_start: 0.6161 (m-80) cc_final: 0.5590 (m-80) REVERT: L 4 MET cc_start: 0.7359 (mmm) cc_final: 0.6622 (mmm) REVERT: L 38 GLN cc_start: 0.7163 (tm-30) cc_final: 0.6557 (tm-30) REVERT: L 53 ASN cc_start: 0.8471 (m110) cc_final: 0.7889 (t0) REVERT: L 70 HIS cc_start: 0.7533 (t70) cc_final: 0.7133 (t-90) REVERT: L 78 LEU cc_start: 0.7766 (tt) cc_final: 0.7429 (mt) REVERT: L 87 TYR cc_start: 0.6785 (m-80) cc_final: 0.6351 (m-80) REVERT: M 38 ARG cc_start: 0.7714 (ptt180) cc_final: 0.7066 (ttp-170) REVERT: M 47 TRP cc_start: 0.7631 (t60) cc_final: 0.6681 (t60) REVERT: M 80 LEU cc_start: 0.8476 (tp) cc_final: 0.8256 (mp) REVERT: N 24 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.7190 (ttm-80) REVERT: N 39 LYS cc_start: 0.8892 (tttm) cc_final: 0.8682 (pttm) REVERT: N 75 ILE cc_start: 0.8074 (mp) cc_final: 0.7670 (mm) REVERT: N 87 TYR cc_start: 0.6669 (m-80) cc_final: 0.6283 (m-10) REVERT: N 91 LEU cc_start: 0.8314 (mt) cc_final: 0.7970 (mp) outliers start: 66 outliers final: 49 residues processed: 490 average time/residue: 0.3639 time to fit residues: 230.7512 Evaluate side-chains 516 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 462 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 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 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 76 GLN 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 24 THR 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 119 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 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 53 LYS 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 L residue 1 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 60 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN G 17 GLN G 52 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.101546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.087268 restraints weight = 30346.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.090253 restraints weight = 17528.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.092305 restraints weight = 11549.883| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9419 Z= 0.202 Angle : 0.864 10.939 12798 Z= 0.437 Chirality : 0.050 0.194 1399 Planarity : 0.006 0.071 1643 Dihedral : 6.495 58.102 1334 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 7.02 % Allowed : 29.38 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1141 helix: -0.32 (0.40), residues: 147 sheet: 0.15 (0.27), residues: 382 loop : -0.57 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP G 35 HIS 0.005 0.002 HIS E 69 PHE 0.031 0.002 PHE D 190 TYR 0.040 0.003 TYR C 137 ARG 0.011 0.001 ARG C 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 2) link_NAG-ASN : angle 2.37592 ( 6) hydrogen bonds : bond 0.03917 ( 368) hydrogen bonds : angle 5.97692 ( 984) SS BOND : bond 0.00553 ( 15) SS BOND : angle 2.31228 ( 30) covalent geometry : bond 0.00458 ( 9402) covalent geometry : angle 0.85682 (12762) *********************** 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: 71 poor density : 469 time to evaluate : 1.636 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: 0.8514 (pm20) cc_final: 0.8136 (pm20) REVERT: B 157 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7535 (p0) REVERT: B 160 ARG cc_start: 0.7106 (ptm-80) cc_final: 0.6235 (ptt90) REVERT: B 162 TYR cc_start: 0.6404 (m-80) cc_final: 0.5844 (m-80) REVERT: C 32 GLU cc_start: 0.3115 (OUTLIER) cc_final: 0.2437 (mp0) REVERT: C 72 GLU cc_start: 0.8042 (tp30) cc_final: 0.7798 (tp30) REVERT: C 104 GLU cc_start: 0.7978 (tt0) cc_final: 0.7558 (tt0) REVERT: C 134 ASN cc_start: 0.7981 (t0) cc_final: 0.7718 (t0) REVERT: C 147 ASP cc_start: 0.8349 (m-30) cc_final: 0.7803 (m-30) REVERT: D 101 GLU cc_start: 0.6027 (pp20) cc_final: 0.5678 (pp20) REVERT: D 102 ARG cc_start: 0.8010 (tmm-80) cc_final: 0.7804 (ttp80) REVERT: D 119 GLN cc_start: 0.8547 (pt0) cc_final: 0.7872 (pm20) REVERT: D 143 ASP cc_start: 0.8664 (m-30) cc_final: 0.8379 (m-30) REVERT: D 151 MET cc_start: 0.7692 (mtt) cc_final: 0.7394 (mtt) REVERT: D 155 GLN cc_start: 0.7439 (tp40) cc_final: 0.6811 (tm-30) REVERT: D 160 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7755 (mtm-85) REVERT: D 165 ASP cc_start: 0.7369 (p0) cc_final: 0.6978 (p0) REVERT: D 171 MET cc_start: 0.7287 (mmm) cc_final: 0.6701 (mmm) REVERT: D 209 HIS cc_start: 0.8443 (m90) cc_final: 0.8059 (m90) REVERT: E 23 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8416 (mm-30) REVERT: E 54 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7232 (mm-30) REVERT: E 73 ASN cc_start: 0.8197 (t0) cc_final: 0.7835 (t0) REVERT: E 121 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7454 (tm-30) REVERT: E 122 PHE cc_start: 0.8401 (p90) cc_final: 0.7983 (p90) REVERT: F 54 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7958 (mmm-85) REVERT: F 66 ARG cc_start: 0.8476 (mtm110) cc_final: 0.8070 (mtp180) REVERT: F 100 TYR cc_start: 0.7405 (t80) cc_final: 0.7027 (t80) REVERT: F 100 MET cc_start: 0.8178 (mtm) cc_final: 0.7775 (mpp) REVERT: G 27 ARG cc_start: 0.8587 (ptt-90) cc_final: 0.8321 (ptt-90) REVERT: G 29 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6539 (m-30) REVERT: G 31 LYS cc_start: 0.8392 (mtmm) cc_final: 0.8116 (mtmm) REVERT: G 53 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7938 (tptp) REVERT: G 54 ARG cc_start: 0.7543 (ttp-110) cc_final: 0.7162 (mtp-110) REVERT: G 60 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8050 (mt-10) REVERT: G 83 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: G 87 TYR cc_start: 0.8058 (m-80) cc_final: 0.7841 (m-80) REVERT: H 27 PHE cc_start: 0.7833 (p90) cc_final: 0.7528 (p90) REVERT: H 34 MET cc_start: 0.7091 (mmm) cc_final: 0.6822 (mmm) REVERT: H 36 TRP cc_start: 0.6506 (m100) cc_final: 0.5914 (m100) REVERT: H 57 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8427 (mtmt) REVERT: H 59 TYR cc_start: 0.7520 (m-80) cc_final: 0.6076 (m-80) REVERT: H 91 PHE cc_start: 0.6200 (m-80) cc_final: 0.5626 (m-80) REVERT: L 4 MET cc_start: 0.7327 (mmm) cc_final: 0.6554 (mmm) REVERT: L 53 ASN cc_start: 0.8502 (m110) cc_final: 0.7959 (t0) REVERT: L 78 LEU cc_start: 0.7789 (tt) cc_final: 0.7381 (mt) REVERT: L 87 TYR cc_start: 0.6786 (m-80) cc_final: 0.6348 (m-80) REVERT: M 38 ARG cc_start: 0.7678 (ptt180) cc_final: 0.7018 (ttp-170) REVERT: M 47 TRP cc_start: 0.7619 (t60) cc_final: 0.6632 (t60) REVERT: M 80 LEU cc_start: 0.8539 (tp) cc_final: 0.8335 (mp) REVERT: N 39 LYS cc_start: 0.8937 (tttm) cc_final: 0.8691 (pttm) REVERT: N 46 LEU cc_start: 0.8632 (tp) cc_final: 0.8000 (pp) REVERT: N 48 ILE cc_start: 0.7891 (mm) cc_final: 0.7444 (mm) REVERT: N 75 ILE cc_start: 0.8095 (mp) cc_final: 0.7701 (mm) REVERT: N 87 TYR cc_start: 0.6680 (m-80) cc_final: 0.6161 (m-10) REVERT: N 91 LEU cc_start: 0.8396 (mt) cc_final: 0.7970 (mp) outliers start: 71 outliers final: 57 residues processed: 489 average time/residue: 0.3899 time to fit residues: 249.4608 Evaluate side-chains 523 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 461 time to evaluate : 3.657 ------------------------------------------------------------------------------- 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 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 76 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 24 THR 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 73 THR 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 48 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 53 LYS 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 48 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 83 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER 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 M residue 94 ARG Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 49 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN G 37 GLN G 52 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.102551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.088043 restraints weight = 30020.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.091122 restraints weight = 17171.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.093242 restraints weight = 11243.570| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9419 Z= 0.174 Angle : 0.887 12.935 12798 Z= 0.440 Chirality : 0.051 0.183 1399 Planarity : 0.006 0.045 1643 Dihedral : 6.394 52.564 1334 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 5.64 % Allowed : 31.36 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1141 helix: -0.27 (0.40), residues: 148 sheet: 0.19 (0.27), residues: 378 loop : -0.60 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP G 35 HIS 0.005 0.001 HIS H 35 PHE 0.022 0.002 PHE D 190 TYR 0.038 0.002 TYR C 137 ARG 0.011 0.001 ARG C 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 2) link_NAG-ASN : angle 2.41462 ( 6) hydrogen bonds : bond 0.03670 ( 368) hydrogen bonds : angle 5.95016 ( 984) SS BOND : bond 0.00859 ( 15) SS BOND : angle 2.11498 ( 30) covalent geometry : bond 0.00406 ( 9402) covalent geometry : angle 0.88031 (12762) *********************** 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 526 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 469 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.8765 (mm) cc_final: 0.8315 (pp) REVERT: B 118 GLN cc_start: 0.8538 (pm20) cc_final: 0.8147 (pm20) REVERT: B 135 MET cc_start: 0.7799 (tmm) cc_final: 0.7429 (tmm) REVERT: B 157 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7624 (p0) REVERT: B 160 ARG cc_start: 0.7155 (ptm-80) cc_final: 0.6091 (ptt90) REVERT: B 162 TYR cc_start: 0.6388 (m-80) cc_final: 0.6066 (m-80) REVERT: C 72 GLU cc_start: 0.8085 (tp30) cc_final: 0.7606 (tp30) REVERT: C 74 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7521 (ttp80) REVERT: C 104 GLU cc_start: 0.8000 (tt0) cc_final: 0.7607 (tt0) REVERT: C 117 LYS cc_start: 0.8602 (pttt) cc_final: 0.8357 (pttt) REVERT: C 134 ASN cc_start: 0.7890 (t0) cc_final: 0.7342 (t0) REVERT: C 147 ASP cc_start: 0.8350 (m-30) cc_final: 0.7785 (m-30) REVERT: D 89 TYR cc_start: 0.7248 (m-80) cc_final: 0.6493 (m-80) REVERT: D 101 GLU cc_start: 0.5868 (pp20) cc_final: 0.5584 (pp20) REVERT: D 119 GLN cc_start: 0.8562 (pt0) cc_final: 0.7873 (pm20) REVERT: D 143 ASP cc_start: 0.8663 (m-30) cc_final: 0.8430 (m-30) REVERT: D 151 MET cc_start: 0.7706 (mtt) cc_final: 0.7387 (mtm) REVERT: D 155 GLN cc_start: 0.7438 (tp40) cc_final: 0.6838 (tm-30) REVERT: D 160 ARG cc_start: 0.8076 (mtm180) cc_final: 0.7751 (mtm110) REVERT: D 165 ASP cc_start: 0.7419 (p0) cc_final: 0.7086 (p0) REVERT: D 171 MET cc_start: 0.7173 (mmm) cc_final: 0.6528 (mmm) REVERT: D 177 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6284 (mm-30) REVERT: D 209 HIS cc_start: 0.8416 (m90) cc_final: 0.8053 (m90) REVERT: E 23 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8440 (mm-30) REVERT: E 54 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7228 (mm-30) REVERT: E 73 ASN cc_start: 0.8120 (t0) cc_final: 0.7709 (t0) REVERT: E 74 PHE cc_start: 0.7481 (t80) cc_final: 0.6826 (t80) REVERT: E 78 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8394 (ttmm) REVERT: E 122 PHE cc_start: 0.8375 (p90) cc_final: 0.8083 (p90) REVERT: F 54 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7962 (mmm-85) REVERT: F 66 ARG cc_start: 0.8515 (mtm110) cc_final: 0.8075 (mtp180) REVERT: F 100 TYR cc_start: 0.7302 (t80) cc_final: 0.6940 (t80) REVERT: F 100 MET cc_start: 0.8185 (mtm) cc_final: 0.7805 (mpp) REVERT: G 27 ARG cc_start: 0.8554 (ptt-90) cc_final: 0.8273 (ptt-90) REVERT: G 29 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6578 (m-30) REVERT: G 31 LYS cc_start: 0.8357 (mtmm) cc_final: 0.7793 (mtmm) REVERT: G 35 TRP cc_start: 0.8445 (m100) cc_final: 0.8195 (m100) REVERT: G 53 LYS cc_start: 0.8355 (mmmm) cc_final: 0.7961 (tptp) REVERT: G 54 ARG cc_start: 0.7613 (ttp-110) cc_final: 0.7169 (mtp-110) REVERT: H 6 GLU cc_start: 0.7582 (mp0) cc_final: 0.6988 (pm20) REVERT: H 27 PHE cc_start: 0.7837 (p90) cc_final: 0.7551 (p90) REVERT: H 34 MET cc_start: 0.7155 (mmm) cc_final: 0.6829 (mmm) REVERT: H 36 TRP cc_start: 0.6339 (m100) cc_final: 0.5789 (m100) REVERT: H 55 ARG cc_start: 0.8087 (mpp80) cc_final: 0.7709 (mtm-85) REVERT: H 57 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8450 (mtmt) REVERT: H 59 TYR cc_start: 0.7578 (m-80) cc_final: 0.6128 (m-80) REVERT: H 91 PHE cc_start: 0.6235 (m-80) cc_final: 0.5636 (m-80) REVERT: L 4 MET cc_start: 0.7273 (mmm) cc_final: 0.6529 (mmm) REVERT: L 31 GLN cc_start: 0.8445 (mp10) cc_final: 0.8026 (pm20) REVERT: L 53 ASN cc_start: 0.8428 (m110) cc_final: 0.7904 (t0) REVERT: L 70 HIS cc_start: 0.7646 (t70) cc_final: 0.7232 (t-90) REVERT: L 78 LEU cc_start: 0.7807 (tt) cc_final: 0.7397 (mt) REVERT: L 87 TYR cc_start: 0.6746 (m-80) cc_final: 0.6408 (m-80) REVERT: L 89 GLN cc_start: 0.7818 (pt0) cc_final: 0.7463 (pt0) REVERT: M 38 ARG cc_start: 0.7656 (ptt180) cc_final: 0.7087 (ttm-80) REVERT: M 47 TRP cc_start: 0.7545 (t60) cc_final: 0.6442 (t60) REVERT: M 80 LEU cc_start: 0.8561 (tp) cc_final: 0.8312 (mp) REVERT: N 39 LYS cc_start: 0.8946 (tttm) cc_final: 0.8709 (pttm) REVERT: N 46 LEU cc_start: 0.8594 (tp) cc_final: 0.8040 (pp) REVERT: N 48 ILE cc_start: 0.7865 (mm) cc_final: 0.7487 (mm) REVERT: N 75 ILE cc_start: 0.8077 (mp) cc_final: 0.7682 (mm) REVERT: N 87 TYR cc_start: 0.6689 (m-80) cc_final: 0.6208 (m-10) REVERT: N 91 LEU cc_start: 0.8323 (mt) cc_final: 0.7976 (mp) outliers start: 57 outliers final: 48 residues processed: 486 average time/residue: 0.4551 time to fit residues: 286.2692 Evaluate side-chains 507 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 456 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 24 THR 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 73 THR 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 29 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 48 VAL 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 91 TYR 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 43 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.0470 chunk 80 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 86 optimal weight: 0.0170 chunk 4 optimal weight: 0.3980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN G 52 ASN H 39 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.089476 restraints weight = 29455.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.092552 restraints weight = 16865.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.094620 restraints weight = 11054.250| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9419 Z= 0.161 Angle : 0.901 14.320 12798 Z= 0.445 Chirality : 0.050 0.183 1399 Planarity : 0.006 0.060 1643 Dihedral : 6.260 43.038 1334 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 5.54 % Allowed : 31.65 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1141 helix: -0.22 (0.41), residues: 147 sheet: 0.17 (0.27), residues: 395 loop : -0.53 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP F 50 HIS 0.006 0.001 HIS L 70 PHE 0.036 0.002 PHE D 74 TYR 0.037 0.002 TYR F 27 ARG 0.017 0.001 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 2) link_NAG-ASN : angle 2.19373 ( 6) hydrogen bonds : bond 0.03637 ( 368) hydrogen bonds : angle 5.88967 ( 984) SS BOND : bond 0.00566 ( 15) SS BOND : angle 1.75657 ( 30) covalent geometry : bond 0.00377 ( 9402) covalent geometry : angle 0.89710 (12762) *********************** 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 518 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 462 time to evaluate : 1.112 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 109 LEU cc_start: 0.8766 (mm) cc_final: 0.8315 (pp) REVERT: B 118 GLN cc_start: 0.8531 (pm20) cc_final: 0.8166 (pm20) REVERT: B 135 MET cc_start: 0.7753 (tmm) cc_final: 0.7440 (tmm) REVERT: B 157 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7596 (p0) REVERT: B 162 TYR cc_start: 0.6362 (m-80) cc_final: 0.6075 (m-80) REVERT: C 72 GLU cc_start: 0.8047 (tp30) cc_final: 0.7754 (tp30) REVERT: C 74 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7504 (ttp80) REVERT: C 80 MET cc_start: 0.7222 (mmt) cc_final: 0.5994 (ttt) REVERT: C 104 GLU cc_start: 0.7950 (tt0) cc_final: 0.7539 (tt0) REVERT: C 121 LEU cc_start: 0.8791 (mp) cc_final: 0.8586 (mm) REVERT: C 147 ASP cc_start: 0.8349 (m-30) cc_final: 0.7711 (m-30) REVERT: D 59 PHE cc_start: 0.8360 (m-80) cc_final: 0.8082 (m-80) REVERT: D 101 GLU cc_start: 0.5844 (pp20) cc_final: 0.5511 (pp20) REVERT: D 119 GLN cc_start: 0.8514 (pt0) cc_final: 0.7844 (pm20) REVERT: D 142 GLU cc_start: 0.8834 (mp0) cc_final: 0.8612 (pm20) REVERT: D 143 ASP cc_start: 0.8704 (m-30) cc_final: 0.8401 (m-30) REVERT: D 151 MET cc_start: 0.7671 (mtt) cc_final: 0.7426 (mtt) REVERT: D 155 GLN cc_start: 0.7388 (tp40) cc_final: 0.6823 (tm-30) REVERT: D 160 ARG cc_start: 0.8028 (mtm180) cc_final: 0.7688 (mtm110) REVERT: D 165 ASP cc_start: 0.7467 (p0) cc_final: 0.7072 (p0) REVERT: D 171 MET cc_start: 0.7061 (mmm) cc_final: 0.6527 (mmm) REVERT: D 177 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6242 (mm-30) REVERT: D 209 HIS cc_start: 0.8380 (m90) cc_final: 0.8017 (m90) REVERT: E 23 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8427 (mm-30) REVERT: E 54 GLU cc_start: 0.7746 (mm-30) cc_final: 0.6956 (mm-30) REVERT: E 73 ASN cc_start: 0.8140 (t0) cc_final: 0.7702 (t0) REVERT: E 78 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8409 (ttmm) REVERT: E 122 PHE cc_start: 0.8343 (p90) cc_final: 0.8140 (p90) REVERT: F 66 ARG cc_start: 0.8476 (mtm110) cc_final: 0.7946 (mtp180) REVERT: F 100 TYR cc_start: 0.7194 (t80) cc_final: 0.6830 (t80) REVERT: F 100 MET cc_start: 0.8193 (mtm) cc_final: 0.7821 (mpp) REVERT: G 27 ARG cc_start: 0.8543 (ptt-90) cc_final: 0.8253 (ptt-90) REVERT: G 29 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6468 (m-30) REVERT: G 35 TRP cc_start: 0.8425 (m100) cc_final: 0.8083 (m100) REVERT: G 54 ARG cc_start: 0.7536 (ttp-110) cc_final: 0.6985 (mtp-110) REVERT: H 6 GLU cc_start: 0.7528 (mp0) cc_final: 0.7113 (pm20) REVERT: H 27 PHE cc_start: 0.7768 (p90) cc_final: 0.7498 (p90) REVERT: H 34 MET cc_start: 0.7099 (mmm) cc_final: 0.6660 (mmm) REVERT: H 36 TRP cc_start: 0.6309 (m100) cc_final: 0.5755 (m100) REVERT: H 59 TYR cc_start: 0.7635 (m-80) cc_final: 0.6206 (m-80) REVERT: H 66 ARG cc_start: 0.6369 (ptm-80) cc_final: 0.4169 (ptm160) REVERT: H 83 ARG cc_start: 0.8323 (tpp80) cc_final: 0.7640 (mpp80) REVERT: H 91 PHE cc_start: 0.6235 (m-80) cc_final: 0.5626 (m-80) REVERT: L 4 MET cc_start: 0.7277 (mmm) cc_final: 0.6560 (mmm) REVERT: L 53 ASN cc_start: 0.8332 (m110) cc_final: 0.7887 (t0) REVERT: L 70 HIS cc_start: 0.7668 (t70) cc_final: 0.7302 (t-90) REVERT: L 75 ILE cc_start: 0.7994 (mp) cc_final: 0.7736 (mp) REVERT: L 87 TYR cc_start: 0.6574 (m-80) cc_final: 0.6319 (m-80) REVERT: L 89 GLN cc_start: 0.7722 (pt0) cc_final: 0.7352 (pt0) REVERT: M 38 ARG cc_start: 0.7660 (ptt180) cc_final: 0.7085 (ttm-80) REVERT: M 46 GLN cc_start: 0.7874 (tp40) cc_final: 0.7344 (tp40) REVERT: M 47 TRP cc_start: 0.7509 (t60) cc_final: 0.6191 (t60) REVERT: M 80 LEU cc_start: 0.8593 (tp) cc_final: 0.8342 (mp) REVERT: N 39 LYS cc_start: 0.8919 (tttm) cc_final: 0.8681 (pttm) REVERT: N 46 LEU cc_start: 0.8578 (tp) cc_final: 0.8053 (pp) REVERT: N 75 ILE cc_start: 0.8030 (mp) cc_final: 0.7629 (mm) REVERT: N 87 TYR cc_start: 0.6591 (m-80) cc_final: 0.6168 (m-10) outliers start: 56 outliers final: 48 residues processed: 481 average time/residue: 0.2754 time to fit residues: 171.4048 Evaluate side-chains 504 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 453 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 58 LYS 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 F residue 111 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 GLN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.102342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.087970 restraints weight = 30193.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.091053 restraints weight = 17225.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.093120 restraints weight = 11252.426| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5589 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= 0.190 Angle : 0.937 15.269 12798 Z= 0.463 Chirality : 0.051 0.187 1399 Planarity : 0.007 0.072 1643 Dihedral : 6.323 36.098 1334 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.95 % Allowed : 32.64 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1141 helix: -0.16 (0.42), residues: 147 sheet: 0.23 (0.27), residues: 377 loop : -0.72 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP F 47 HIS 0.004 0.001 HIS L 70 PHE 0.037 0.002 PHE D 74 TYR 0.034 0.002 TYR F 27 ARG 0.022 0.001 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 2) link_NAG-ASN : angle 2.35560 ( 6) hydrogen bonds : bond 0.03756 ( 368) hydrogen bonds : angle 6.01930 ( 984) SS BOND : bond 0.00616 ( 15) SS BOND : angle 1.95569 ( 30) covalent geometry : bond 0.00437 ( 9402) covalent geometry : angle 0.93185 (12762) ********************** 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 511 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 461 time to evaluate : 1.032 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: 0.8481 (pm20) cc_final: 0.8125 (pm20) REVERT: B 135 MET cc_start: 0.7800 (tmm) cc_final: 0.7463 (tmm) REVERT: B 157 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7588 (p0) REVERT: B 162 TYR cc_start: 0.6553 (m-80) cc_final: 0.6072 (m-80) REVERT: C 72 GLU cc_start: 0.8055 (tp30) cc_final: 0.7763 (tp30) REVERT: C 74 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7772 (ttp80) REVERT: C 80 MET cc_start: 0.7365 (mmt) cc_final: 0.6600 (ttt) REVERT: C 104 GLU cc_start: 0.7970 (tt0) cc_final: 0.7685 (tt0) REVERT: C 120 TYR cc_start: 0.8456 (m-10) cc_final: 0.8248 (m-10) REVERT: C 121 LEU cc_start: 0.8752 (mp) cc_final: 0.8500 (mm) REVERT: C 147 ASP cc_start: 0.8229 (m-30) cc_final: 0.7855 (m-30) REVERT: D 119 GLN cc_start: 0.8526 (pt0) cc_final: 0.7817 (pm20) REVERT: D 143 ASP cc_start: 0.8716 (m-30) cc_final: 0.8452 (m-30) REVERT: D 151 MET cc_start: 0.7689 (mtt) cc_final: 0.7474 (mtt) REVERT: D 155 GLN cc_start: 0.7407 (tp40) cc_final: 0.6850 (tm-30) REVERT: D 160 ARG cc_start: 0.8003 (mtm180) cc_final: 0.7649 (mtm110) REVERT: D 165 ASP cc_start: 0.7475 (p0) cc_final: 0.7081 (p0) REVERT: D 171 MET cc_start: 0.7051 (mmm) cc_final: 0.6547 (mmm) REVERT: D 177 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6329 (mm-30) REVERT: D 209 HIS cc_start: 0.8314 (m90) cc_final: 0.8009 (m90) REVERT: D 212 LEU cc_start: 0.8889 (mm) cc_final: 0.8607 (mm) REVERT: E 23 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8407 (mm-30) REVERT: E 54 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7262 (mm-30) REVERT: E 73 ASN cc_start: 0.8271 (t0) cc_final: 0.7846 (t0) REVERT: E 78 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8466 (ttmm) REVERT: F 80 MET cc_start: 0.6983 (tmm) cc_final: 0.6525 (ttp) REVERT: F 100 TYR cc_start: 0.7314 (t80) cc_final: 0.6975 (t80) REVERT: F 100 MET cc_start: 0.8187 (mtm) cc_final: 0.7789 (mpp) REVERT: G 27 ARG cc_start: 0.8518 (ptt-90) cc_final: 0.8164 (ptt-90) REVERT: G 29 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6613 (m-30) REVERT: G 31 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8190 (mtmm) REVERT: G 35 TRP cc_start: 0.8421 (m100) cc_final: 0.8021 (m100) REVERT: G 60 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7753 (mm-30) REVERT: G 86 TYR cc_start: 0.8217 (m-10) cc_final: 0.7735 (m-80) REVERT: H 27 PHE cc_start: 0.7785 (p90) cc_final: 0.7579 (p90) REVERT: H 34 MET cc_start: 0.7130 (mmm) cc_final: 0.6663 (mmm) REVERT: H 36 TRP cc_start: 0.5861 (m100) cc_final: 0.5378 (m100) REVERT: H 59 TYR cc_start: 0.7148 (m-80) cc_final: 0.6517 (m-80) REVERT: H 83 ARG cc_start: 0.8372 (tpp80) cc_final: 0.7785 (mpp80) REVERT: H 91 PHE cc_start: 0.6174 (m-80) cc_final: 0.5540 (m-80) REVERT: H 102 VAL cc_start: 0.7743 (t) cc_final: 0.7538 (t) REVERT: L 4 MET cc_start: 0.7412 (mmm) cc_final: 0.6160 (mmp) REVERT: L 31 GLN cc_start: 0.8531 (mp10) cc_final: 0.7947 (pm20) REVERT: L 53 ASN cc_start: 0.8290 (m110) cc_final: 0.7875 (t0) REVERT: L 70 HIS cc_start: 0.7646 (t70) cc_final: 0.7208 (t-90) REVERT: L 75 ILE cc_start: 0.8064 (mp) cc_final: 0.7759 (mp) REVERT: L 78 LEU cc_start: 0.7787 (tt) cc_final: 0.7386 (mt) REVERT: L 87 TYR cc_start: 0.6741 (m-80) cc_final: 0.6431 (m-80) REVERT: M 38 ARG cc_start: 0.7661 (ptt180) cc_final: 0.7102 (ttm-80) REVERT: M 46 GLN cc_start: 0.7936 (tp40) cc_final: 0.7434 (tp40) REVERT: M 47 TRP cc_start: 0.7516 (t60) cc_final: 0.6149 (t60) REVERT: M 80 LEU cc_start: 0.8532 (tp) cc_final: 0.8299 (mp) REVERT: N 6 GLN cc_start: 0.7079 (mt0) cc_final: 0.6237 (mt0) REVERT: N 39 LYS cc_start: 0.8943 (tttm) cc_final: 0.8708 (pttm) REVERT: N 46 LEU cc_start: 0.8603 (tp) cc_final: 0.8107 (pp) REVERT: N 75 ILE cc_start: 0.8070 (mp) cc_final: 0.7676 (mm) REVERT: N 87 TYR cc_start: 0.6625 (m-80) cc_final: 0.6128 (m-10) REVERT: N 91 LEU cc_start: 0.8180 (mt) cc_final: 0.7782 (mp) outliers start: 50 outliers final: 43 residues processed: 477 average time/residue: 0.2817 time to fit residues: 174.9707 Evaluate side-chains 501 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 455 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 ARG 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 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 24 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 58 LYS 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 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 52 ASN Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 91 TYR 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 16 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 0.0000 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN G 52 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.102299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.087999 restraints weight = 30461.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.091077 restraints weight = 17573.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.093157 restraints weight = 11539.118| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 9419 Z= 0.323 Angle : 1.230 59.196 12798 Z= 0.684 Chirality : 0.051 0.266 1399 Planarity : 0.007 0.070 1643 Dihedral : 6.335 36.035 1334 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 28.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.85 % Allowed : 33.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1141 helix: -0.17 (0.42), residues: 147 sheet: 0.14 (0.27), residues: 383 loop : -0.69 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP D 106 HIS 0.004 0.001 HIS L 70 PHE 0.034 0.002 PHE D 74 TYR 0.029 0.002 TYR F 27 ARG 0.030 0.001 ARG G 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 2) link_NAG-ASN : angle 2.35361 ( 6) hydrogen bonds : bond 0.03772 ( 368) hydrogen bonds : angle 6.02767 ( 984) SS BOND : bond 0.00802 ( 15) SS BOND : angle 3.19316 ( 30) covalent geometry : bond 0.00643 ( 9402) covalent geometry : angle 1.22114 (12762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5351.82 seconds wall clock time: 100 minutes 26.58 seconds (6026.58 seconds total)