Starting phenix.real_space_refine on Fri Sep 11 13:27:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vja_21212/09_2026/6vja_21212.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vja_21212/09_2026/6vja_21212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vja_21212/09_2026/6vja_21212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vja_21212/09_2026/6vja_21212.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vja_21212/09_2026/6vja_21212.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vja_21212/09_2026/6vja_21212.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vja_21212/09_2026/6vja_21212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vja_21212/09_2026/6vja_21212.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6004 2.51 5 N 1500 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9342 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1275 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "D" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1275 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1668 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "I" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1668 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "L" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1623 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199} Chain: "M" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1623 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.37, per 1000 atoms: 0.25 Number of scatterers: 9342 At special positions: 0 Unit cell: (161, 70, 132, 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 56 16.00 O 1782 8.00 N 1500 7.00 C 6004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 167 " - pdb=" SG CYS D 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.05 Simple disulfide: pdb=" SG CYS H 216 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.05 Simple disulfide: pdb=" SG CYS I 216 " - pdb=" SG CYS M 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " 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 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 359.3 milliseconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 22 sheets defined 27.6% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'C' and resid 47 through 71 removed outlier: 4.541A pdb=" N THR C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 63 " --> pdb=" O ASN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 85 through 97 removed outlier: 3.867A pdb=" N TRP C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 114 through 143 removed outlier: 3.759A pdb=" N ILE C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 177 through 206 removed outlier: 3.770A pdb=" N GLN C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN C 204 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 71 removed outlier: 4.406A pdb=" N THR D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS D 63 " --> pdb=" O ASN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.606A pdb=" N TRP D 89 " --> pdb=" O TRP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 114 through 141 removed outlier: 3.559A pdb=" N ILE D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 124 " --> pdb=" O ASN D 120 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 177 through 206 removed outlier: 3.591A pdb=" N GLN D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.838A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 removed outlier: 4.458A pdb=" N GLY H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.707A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 129 No H-bonds generated for 'chain 'H' and resid 127 through 129' Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.797A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 4.410A pdb=" N GLY I 65 " --> pdb=" O GLN I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.706A pdb=" N SER I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'I' and resid 156 through 158 No H-bonds generated for 'chain 'I' and resid 156 through 158' Processing helix chain 'I' and resid 187 through 189 No H-bonds generated for 'chain 'I' and resid 187 through 189' Processing helix chain 'I' and resid 201 through 204 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.970A pdb=" N ALA L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.928A pdb=" N ALA M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.863A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.554A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN H 33 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.554A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG H 94 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.572A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 132 removed outlier: 6.011A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.020A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.882A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.552A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN I 33 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.552A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG I 94 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP I 100A" --> pdb=" O TYR I 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 120 through 124 removed outlier: 5.978A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 131 through 132 removed outlier: 5.978A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 151 through 154 removed outlier: 4.019A pdb=" N TYR I 194 " --> pdb=" O VAL I 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.544A pdb=" N TRP L 35 " --> pdb=" O TRP L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.582A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.790A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA L 130 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.518A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'M' and resid 10 through 13 removed outlier: 4.158A pdb=" N ALA M 13 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP M 35 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 10 through 13 removed outlier: 4.158A pdb=" N ALA M 13 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 114 through 118 removed outlier: 3.781A pdb=" N VAL M 133 " --> pdb=" O PHE M 118 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA M 130 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 153 through 154 removed outlier: 3.507A pdb=" N CYS M 194 " --> pdb=" O LYS M 207 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS M 207 " --> pdb=" O CYS M 194 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2301 1.33 - 1.46: 2388 1.46 - 1.58: 4809 1.58 - 1.71: 0 1.71 - 1.84: 84 Bond restraints: 9582 Sorted by residual: bond pdb=" CAX Y01 D 402 " pdb=" OAH Y01 D 402 " ideal model delta sigma weight residual 1.248 1.343 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" CAX Y01 C1001 " pdb=" OAH Y01 C1001 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CAX Y01 D 403 " pdb=" OAH Y01 D 403 " ideal model delta sigma weight residual 1.248 1.340 -0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" CAX Y01 D 401 " pdb=" OAH Y01 D 401 " ideal model delta sigma weight residual 1.248 1.340 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" CAX Y01 C1003 " pdb=" OAH Y01 C1003 " ideal model delta sigma weight residual 1.248 1.338 -0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 9577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 12012 2.20 - 4.39: 893 4.39 - 6.59: 117 6.59 - 8.78: 32 8.78 - 10.98: 4 Bond angle restraints: 13058 Sorted by residual: angle pdb=" CA TRP M 91 " pdb=" CB TRP M 91 " pdb=" CG TRP M 91 " ideal model delta sigma weight residual 113.60 122.09 -8.49 1.90e+00 2.77e-01 2.00e+01 angle pdb=" CA TYR H 100C" pdb=" CB TYR H 100C" pdb=" CG TYR H 100C" ideal model delta sigma weight residual 113.90 121.28 -7.38 1.80e+00 3.09e-01 1.68e+01 angle pdb=" CA TRP L 91 " pdb=" CB TRP L 91 " pdb=" CG TRP L 91 " ideal model delta sigma weight residual 113.60 121.04 -7.44 1.90e+00 2.77e-01 1.53e+01 angle pdb=" CA TYR I 100C" pdb=" CB TYR I 100C" pdb=" CG TYR I 100C" ideal model delta sigma weight residual 113.90 120.93 -7.03 1.80e+00 3.09e-01 1.53e+01 angle pdb=" N LEU D 112 " pdb=" CA LEU D 112 " pdb=" C LEU D 112 " ideal model delta sigma weight residual 110.80 102.49 8.31 2.13e+00 2.20e-01 1.52e+01 ... (remaining 13053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5339 17.90 - 35.80: 256 35.80 - 53.70: 42 53.70 - 71.60: 26 71.60 - 89.49: 12 Dihedral angle restraints: 5675 sinusoidal: 2195 harmonic: 3480 Sorted by residual: dihedral pdb=" CB CYS C 167 " pdb=" SG CYS C 167 " pdb=" SG CYS C 183 " pdb=" CB CYS C 183 " ideal model delta sinusoidal sigma weight residual -86.00 -149.42 63.42 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS D 167 " pdb=" SG CYS D 167 " pdb=" SG CYS D 183 " pdb=" CB CYS D 183 " ideal model delta sinusoidal sigma weight residual -86.00 -148.59 62.59 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CA ASN D 166 " pdb=" C ASN D 166 " pdb=" N CYS D 167 " pdb=" CA CYS D 167 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 5672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1277 0.100 - 0.199: 187 0.199 - 0.299: 10 0.299 - 0.398: 10 0.398 - 0.498: 6 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CBG Y01 D 403 " pdb=" CAQ Y01 D 403 " pdb=" CBD Y01 D 403 " pdb=" CBI Y01 D 403 " both_signs ideal model delta sigma weight residual False -2.33 -2.83 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CBG Y01 C1003 " pdb=" CAQ Y01 C1003 " pdb=" CBD Y01 C1003 " pdb=" CBI Y01 C1003 " both_signs ideal model delta sigma weight residual False -2.33 -2.82 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CBG Y01 D 401 " pdb=" CAQ Y01 D 401 " pdb=" CBD Y01 D 401 " pdb=" CBI Y01 D 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.48 2.00e-01 2.50e+01 5.74e+00 ... (remaining 1487 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 94 " 0.099 9.50e-02 1.11e+02 5.41e-02 1.32e+01 pdb=" NE ARG H 94 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG H 94 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG H 94 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG H 94 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 120 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C ASN D 120 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN D 120 " -0.020 2.00e-02 2.50e+03 pdb=" N SER D 121 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 91 " -0.027 2.00e-02 2.50e+03 1.94e-02 9.44e+00 pdb=" CG TRP M 91 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP M 91 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP M 91 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP M 91 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 91 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP M 91 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 91 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 91 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP M 91 " -0.004 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1000 2.73 - 3.28: 8990 3.28 - 3.82: 14171 3.82 - 4.36: 17033 4.36 - 4.90: 29761 Nonbonded interactions: 70955 Sorted by model distance: nonbonded pdb=" OE2 GLU M 105 " pdb=" OH TYR M 173 " model vdw 2.193 3.040 nonbonded pdb=" OE1 GLU D 168 " pdb=" OH TYR D 184 " model vdw 2.271 3.040 nonbonded pdb=" OE2 GLU L 105 " pdb=" OH TYR L 173 " model vdw 2.296 3.040 nonbonded pdb=" ND2 ASN M 210 " pdb=" OE1 GLU M 213 " model vdw 2.299 3.120 nonbonded pdb=" N GLU L 79 " pdb=" OD2 ASP L 82 " model vdw 2.328 3.120 ... (remaining 70950 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.630 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.014 0.117 9593 Z= 0.585 Angle : 1.273 10.980 13080 Z= 0.674 Chirality : 0.078 0.498 1490 Planarity : 0.007 0.060 1608 Dihedral : 12.509 89.494 3418 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 0.49 % Allowed : 1.46 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1192 helix: -0.71 (0.29), residues: 234 sheet: 1.98 (0.26), residues: 372 loop : -0.07 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.007 ARG H 94 TYR 0.038 0.007 TYR I 100C PHE 0.040 0.004 PHE H 100D TRP 0.052 0.005 TRP M 91 HIS 0.011 0.003 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.01370 / 0.59 ( 9582) covalent geometry : angle 1.27006 / 0.67 (13058) SS BOND : bond 0.01058 / 0.66 ( 11) SS BOND : angle 2.51481 / 1.65 ( 22) hydrogen bonds : bond 0.21402 / 14.09 ( 434) hydrogen bonds : angle 8.48481 / 6.03 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 301 time to evaluate : 0.402 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: C 113 VAL cc_start: 0.5993 (m) cc_final: 0.5431 (t) REVERT: C 116 LYS cc_start: 0.8669 (mttt) cc_final: 0.8354 (mttt) REVERT: C 147 LEU cc_start: 0.7698 (mt) cc_final: 0.7358 (mp) REVERT: C 175 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8366 (mmtp) REVERT: D 58 MET cc_start: 0.9273 (mmp) cc_final: 0.9008 (mmm) REVERT: D 89 TRP cc_start: 0.8880 (OUTLIER) cc_final: 0.8337 (p90) REVERT: H 5 GLN cc_start: 0.8690 (tt0) cc_final: 0.8434 (tp40) REVERT: H 64 LYS cc_start: 0.8666 (tttt) cc_final: 0.8323 (ttpp) REVERT: H 72 ASP cc_start: 0.8158 (t0) cc_final: 0.7738 (t0) REVERT: H 77 THR cc_start: 0.9088 (m) cc_final: 0.8498 (p) REVERT: H 86 ASP cc_start: 0.8579 (m-30) cc_final: 0.8011 (m-30) REVERT: H 154 TRP cc_start: 0.8131 (m100) cc_final: 0.7790 (m100) REVERT: I 64 LYS cc_start: 0.8730 (tttt) cc_final: 0.8386 (ttpp) REVERT: I 72 ASP cc_start: 0.8162 (t0) cc_final: 0.7791 (t0) REVERT: I 77 THR cc_start: 0.8981 (m) cc_final: 0.8433 (p) REVERT: I 86 ASP cc_start: 0.8475 (m-30) cc_final: 0.7910 (m-30) REVERT: I 154 TRP cc_start: 0.8036 (m100) cc_final: 0.7734 (m100) REVERT: I 161 SER cc_start: 0.8296 (m) cc_final: 0.7886 (p) REVERT: I 214 LYS cc_start: 0.8374 (mttt) cc_final: 0.7822 (tptt) REVERT: L 82 ASP cc_start: 0.8242 (m-30) cc_final: 0.7847 (m-30) REVERT: L 117 ILE cc_start: 0.8791 (tt) cc_final: 0.8457 (tt) REVERT: L 118 PHE cc_start: 0.8244 (m-80) cc_final: 0.7475 (m-80) REVERT: L 124 GLN cc_start: 0.8046 (tt0) cc_final: 0.7816 (tt0) REVERT: L 126 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7629 (tppt) REVERT: M 24 ARG cc_start: 0.8363 (ttm110) cc_final: 0.7959 (ttp80) REVERT: M 82 ASP cc_start: 0.8188 (m-30) cc_final: 0.7828 (m-30) REVERT: M 118 PHE cc_start: 0.8278 (m-80) cc_final: 0.7450 (m-80) REVERT: M 124 GLN cc_start: 0.7880 (tt0) cc_final: 0.7661 (tt0) REVERT: M 126 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7822 (tppt) REVERT: M 214 CYS cc_start: 0.3960 (t) cc_final: 0.3737 (t) outliers start: 5 outliers final: 1 residues processed: 306 average time/residue: 0.0919 time to fit residues: 39.8734 Evaluate side-chains 225 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain D residue 89 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.0040 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 GLN C 59 ASN C 181 GLN C 204 GLN D 56 GLN D 63 HIS D 181 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN L 124 GLN M 53 ASN M 124 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.159074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.109937 restraints weight = 15949.866| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.49 r_work: 0.3218 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9593 Z= 0.132 Angle : 0.661 9.192 13080 Z= 0.336 Chirality : 0.043 0.167 1490 Planarity : 0.004 0.043 1608 Dihedral : 6.623 59.523 1362 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.05 % Allowed : 10.84 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1192 helix: 1.02 (0.33), residues: 248 sheet: 2.19 (0.25), residues: 404 loop : 0.38 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 109 TYR 0.038 0.002 TYR C 94 PHE 0.014 0.001 PHE I 122 TRP 0.019 0.002 TRP D 89 HIS 0.004 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9582) covalent geometry : angle 0.65723 / 0.33 (13058) SS BOND : bond 0.00937 / 0.61 ( 11) SS BOND : angle 1.76426 / 0.96 ( 22) hydrogen bonds : bond 0.04796 / 3.24 ( 434) hydrogen bonds : angle 5.48866 / 3.88 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8528 (mttt) cc_final: 0.8106 (mmmt) REVERT: C 139 LEU cc_start: 0.8965 (mm) cc_final: 0.8629 (mm) REVERT: C 175 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8230 (mmtp) REVERT: D 62 PHE cc_start: 0.8711 (t80) cc_final: 0.8424 (t80) REVERT: D 89 TRP cc_start: 0.8765 (OUTLIER) cc_final: 0.7648 (p90) REVERT: D 116 LYS cc_start: 0.8234 (mttt) cc_final: 0.7665 (mttt) REVERT: D 175 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8354 (mmtp) REVERT: H 5 GLN cc_start: 0.8623 (tt0) cc_final: 0.8196 (tp40) REVERT: H 64 LYS cc_start: 0.8706 (tttt) cc_final: 0.8304 (ttpp) REVERT: H 72 ASP cc_start: 0.8120 (t0) cc_final: 0.7606 (t0) REVERT: H 77 THR cc_start: 0.8926 (m) cc_final: 0.8316 (p) REVERT: H 86 ASP cc_start: 0.8418 (m-30) cc_final: 0.8147 (m-30) REVERT: H 154 TRP cc_start: 0.8087 (m100) cc_final: 0.7672 (m100) REVERT: I 5 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: I 64 LYS cc_start: 0.8848 (tttt) cc_final: 0.8436 (ttpp) REVERT: I 72 ASP cc_start: 0.8135 (t0) cc_final: 0.7694 (t0) REVERT: I 77 THR cc_start: 0.8958 (m) cc_final: 0.8354 (p) REVERT: I 86 ASP cc_start: 0.8321 (m-30) cc_final: 0.7963 (m-30) REVERT: I 122 PHE cc_start: 0.7327 (m-10) cc_final: 0.7069 (m-10) REVERT: I 154 TRP cc_start: 0.8116 (m100) cc_final: 0.7697 (m100) REVERT: I 161 SER cc_start: 0.8134 (m) cc_final: 0.7734 (p) REVERT: I 214 LYS cc_start: 0.8479 (mttt) cc_final: 0.7973 (tptt) REVERT: L 24 ARG cc_start: 0.8076 (ttp-110) cc_final: 0.7857 (ttp80) REVERT: L 79 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7079 (mt-10) REVERT: L 82 ASP cc_start: 0.8790 (m-30) cc_final: 0.8447 (m-30) REVERT: L 118 PHE cc_start: 0.8633 (m-80) cc_final: 0.7762 (m-80) REVERT: L 124 GLN cc_start: 0.7955 (tt0) cc_final: 0.7389 (tt0) REVERT: M 24 ARG cc_start: 0.8425 (ttm110) cc_final: 0.8113 (ttp80) REVERT: M 79 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7165 (mt-10) REVERT: M 82 ASP cc_start: 0.8811 (m-30) cc_final: 0.8476 (m-30) REVERT: M 118 PHE cc_start: 0.8568 (m-80) cc_final: 0.7765 (m-80) REVERT: M 124 GLN cc_start: 0.7835 (tt0) cc_final: 0.7399 (tt0) outliers start: 21 outliers final: 11 residues processed: 274 average time/residue: 0.0885 time to fit residues: 34.9304 Evaluate side-chains 232 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 219 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 181 GLN H 1 GLN L 160 GLN M 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.158196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107679 restraints weight = 15926.228| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.51 r_work: 0.3146 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9593 Z= 0.162 Angle : 0.638 8.449 13080 Z= 0.324 Chirality : 0.043 0.182 1490 Planarity : 0.005 0.048 1608 Dihedral : 6.253 56.111 1362 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.20 % Allowed : 12.01 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1192 helix: 1.35 (0.34), residues: 246 sheet: 2.07 (0.26), residues: 372 loop : 0.41 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 109 TYR 0.042 0.002 TYR C 94 PHE 0.014 0.001 PHE H 100D TRP 0.019 0.002 TRP D 89 HIS 0.004 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 9582) covalent geometry : angle 0.62919 / 0.32 (13058) SS BOND : bond 0.00504 / 0.34 ( 11) SS BOND : angle 2.69553 / 1.35 ( 22) hydrogen bonds : bond 0.04321 / 2.92 ( 434) hydrogen bonds : angle 5.00056 / 3.55 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8541 (mttt) cc_final: 0.8202 (mmmt) REVERT: D 62 PHE cc_start: 0.8597 (t80) cc_final: 0.8246 (t80) REVERT: D 116 LYS cc_start: 0.8373 (mttt) cc_final: 0.7836 (mttt) REVERT: H 5 GLN cc_start: 0.8545 (tt0) cc_final: 0.8123 (tp40) REVERT: H 64 LYS cc_start: 0.8983 (tttt) cc_final: 0.8553 (ttpp) REVERT: H 72 ASP cc_start: 0.8268 (t0) cc_final: 0.7730 (t0) REVERT: H 77 THR cc_start: 0.8947 (m) cc_final: 0.8352 (p) REVERT: H 85 GLU cc_start: 0.9166 (tp30) cc_final: 0.8896 (tp30) REVERT: H 86 ASP cc_start: 0.8437 (m-30) cc_final: 0.8034 (m-30) REVERT: H 154 TRP cc_start: 0.8300 (m100) cc_final: 0.7864 (m100) REVERT: H 195 ILE cc_start: 0.7173 (mm) cc_final: 0.6933 (tp) REVERT: I 64 LYS cc_start: 0.9027 (tttt) cc_final: 0.8607 (ttpp) REVERT: I 72 ASP cc_start: 0.8343 (t0) cc_final: 0.7828 (t0) REVERT: I 77 THR cc_start: 0.8947 (m) cc_final: 0.8337 (p) REVERT: I 86 ASP cc_start: 0.8342 (m-30) cc_final: 0.7930 (m-30) REVERT: I 97 TYR cc_start: 0.9036 (t80) cc_final: 0.8732 (t80) REVERT: I 154 TRP cc_start: 0.8285 (m100) cc_final: 0.7785 (m100) REVERT: I 161 SER cc_start: 0.8184 (m) cc_final: 0.7845 (p) REVERT: I 214 LYS cc_start: 0.8471 (mttt) cc_final: 0.7942 (tptt) REVERT: L 79 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7098 (mt-10) REVERT: L 82 ASP cc_start: 0.8796 (m-30) cc_final: 0.8431 (m-30) REVERT: L 118 PHE cc_start: 0.8566 (m-80) cc_final: 0.7717 (m-80) REVERT: L 124 GLN cc_start: 0.7930 (tt0) cc_final: 0.7258 (tt0) REVERT: M 24 ARG cc_start: 0.8412 (ttm110) cc_final: 0.8101 (ttp80) REVERT: M 79 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7162 (mt-10) REVERT: M 82 ASP cc_start: 0.8787 (m-30) cc_final: 0.8427 (m-30) REVERT: M 118 PHE cc_start: 0.8580 (m-80) cc_final: 0.7817 (m-80) REVERT: M 124 GLN cc_start: 0.7788 (tt0) cc_final: 0.7373 (tt0) REVERT: M 126 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7854 (tppt) REVERT: M 148 TRP cc_start: 0.6767 (m100) cc_final: 0.6555 (m100) outliers start: 43 outliers final: 30 residues processed: 250 average time/residue: 0.0838 time to fit residues: 30.6315 Evaluate side-chains 235 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 63 HIS Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN I 1 GLN M 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105429 restraints weight = 16134.641| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.58 r_work: 0.3118 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9593 Z= 0.231 Angle : 0.676 7.923 13080 Z= 0.343 Chirality : 0.044 0.170 1490 Planarity : 0.005 0.046 1608 Dihedral : 6.308 53.187 1362 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.39 % Allowed : 14.65 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.24), residues: 1192 helix: 1.22 (0.33), residues: 246 sheet: 2.02 (0.26), residues: 368 loop : 0.15 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 109 TYR 0.043 0.002 TYR C 94 PHE 0.015 0.002 PHE I 100D TRP 0.019 0.002 TRP D 89 HIS 0.004 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 ( 9582) covalent geometry : angle 0.67125 / 0.34 (13058) SS BOND : bond 0.00596 / 0.40 ( 11) SS BOND : angle 2.03752 / 1.09 ( 22) hydrogen bonds : bond 0.04703 / 3.18 ( 434) hydrogen bonds : angle 5.08513 / 3.60 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8646 (mttt) cc_final: 0.8311 (mmmt) REVERT: C 175 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8411 (mmtp) REVERT: C 197 MET cc_start: 0.9632 (ttm) cc_final: 0.9389 (ttp) REVERT: D 116 LYS cc_start: 0.8479 (mttt) cc_final: 0.7939 (mttt) REVERT: D 139 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8737 (mm) REVERT: D 175 LYS cc_start: 0.8758 (mmtp) cc_final: 0.8510 (mmtp) REVERT: D 197 MET cc_start: 0.9599 (ttm) cc_final: 0.9346 (ttp) REVERT: H 5 GLN cc_start: 0.8600 (tt0) cc_final: 0.8172 (tp40) REVERT: H 64 LYS cc_start: 0.9083 (tttt) cc_final: 0.8654 (ttpp) REVERT: H 72 ASP cc_start: 0.8276 (t0) cc_final: 0.7759 (t0) REVERT: H 77 THR cc_start: 0.9013 (m) cc_final: 0.8366 (p) REVERT: H 85 GLU cc_start: 0.9129 (tp30) cc_final: 0.8926 (tp30) REVERT: H 86 ASP cc_start: 0.8421 (m-30) cc_final: 0.8059 (m-30) REVERT: H 161 SER cc_start: 0.8140 (m) cc_final: 0.7783 (p) REVERT: I 64 LYS cc_start: 0.9089 (tttt) cc_final: 0.8627 (ttpp) REVERT: I 72 ASP cc_start: 0.8336 (t0) cc_final: 0.7834 (t0) REVERT: I 77 THR cc_start: 0.9020 (m) cc_final: 0.8344 (p) REVERT: I 86 ASP cc_start: 0.8331 (m-30) cc_final: 0.7916 (m-30) REVERT: I 97 TYR cc_start: 0.9131 (t80) cc_final: 0.8885 (t80) REVERT: I 154 TRP cc_start: 0.8379 (m100) cc_final: 0.7856 (m100) REVERT: I 161 SER cc_start: 0.8210 (m) cc_final: 0.7859 (p) REVERT: I 214 LYS cc_start: 0.8410 (mttt) cc_final: 0.7886 (tptt) REVERT: L 79 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7303 (mt-10) REVERT: L 82 ASP cc_start: 0.8848 (m-30) cc_final: 0.8410 (m-30) REVERT: L 118 PHE cc_start: 0.8586 (m-80) cc_final: 0.7806 (m-80) REVERT: L 124 GLN cc_start: 0.7892 (tt0) cc_final: 0.7266 (tt0) REVERT: M 24 ARG cc_start: 0.8463 (ttm110) cc_final: 0.8125 (ttp80) REVERT: M 79 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7362 (mt-10) REVERT: M 82 ASP cc_start: 0.8821 (m-30) cc_final: 0.8405 (m-30) REVERT: M 118 PHE cc_start: 0.8487 (m-80) cc_final: 0.7614 (m-80) REVERT: M 124 GLN cc_start: 0.7591 (tt0) cc_final: 0.7030 (tt0) REVERT: M 126 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7785 (tppt) REVERT: M 158 ASN cc_start: 0.7619 (t160) cc_final: 0.6561 (p0) outliers start: 45 outliers final: 31 residues processed: 235 average time/residue: 0.0824 time to fit residues: 28.0239 Evaluate side-chains 227 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 63 HIS Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107220 restraints weight = 15925.093| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.47 r_work: 0.3178 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9593 Z= 0.155 Angle : 0.607 10.365 13080 Z= 0.304 Chirality : 0.042 0.171 1490 Planarity : 0.005 0.045 1608 Dihedral : 5.918 56.204 1362 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.10 % Allowed : 15.23 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.24), residues: 1192 helix: 1.48 (0.33), residues: 246 sheet: 1.87 (0.25), residues: 382 loop : 0.03 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 109 TYR 0.045 0.002 TYR C 94 PHE 0.015 0.001 PHE C 62 TRP 0.020 0.001 TRP D 89 HIS 0.003 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 9582) covalent geometry : angle 0.60328 / 0.30 (13058) SS BOND : bond 0.00543 / 0.35 ( 11) SS BOND : angle 1.64481 / 0.83 ( 22) hydrogen bonds : bond 0.03973 / 2.69 ( 434) hydrogen bonds : angle 4.75177 / 3.35 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8644 (OUTLIER) cc_final: 0.7336 (p90) REVERT: C 116 LYS cc_start: 0.8642 (mttt) cc_final: 0.8275 (mmmt) REVERT: C 197 MET cc_start: 0.9626 (ttm) cc_final: 0.9367 (ttp) REVERT: D 116 LYS cc_start: 0.8393 (mttt) cc_final: 0.7845 (mttt) REVERT: D 197 MET cc_start: 0.9603 (ttm) cc_final: 0.9356 (ttp) REVERT: H 5 GLN cc_start: 0.8581 (tt0) cc_final: 0.8151 (tp40) REVERT: H 64 LYS cc_start: 0.8995 (tttt) cc_final: 0.8560 (ttpp) REVERT: H 72 ASP cc_start: 0.8218 (t0) cc_final: 0.7679 (t0) REVERT: H 77 THR cc_start: 0.8977 (m) cc_final: 0.8390 (p) REVERT: H 85 GLU cc_start: 0.9118 (tp30) cc_final: 0.8891 (tp30) REVERT: H 86 ASP cc_start: 0.8342 (m-30) cc_final: 0.7919 (m-30) REVERT: H 154 TRP cc_start: 0.8428 (m100) cc_final: 0.8139 (m100) REVERT: H 161 SER cc_start: 0.8049 (m) cc_final: 0.7718 (p) REVERT: H 199 ASN cc_start: 0.7091 (t0) cc_final: 0.6885 (t0) REVERT: I 64 LYS cc_start: 0.8989 (tttt) cc_final: 0.8529 (ttpp) REVERT: I 72 ASP cc_start: 0.8271 (t0) cc_final: 0.7727 (t0) REVERT: I 77 THR cc_start: 0.8990 (m) cc_final: 0.8376 (p) REVERT: I 86 ASP cc_start: 0.8249 (m-30) cc_final: 0.7812 (m-30) REVERT: I 97 TYR cc_start: 0.8996 (t80) cc_final: 0.8650 (t80) REVERT: I 154 TRP cc_start: 0.8383 (m100) cc_final: 0.7946 (m100) REVERT: I 161 SER cc_start: 0.8152 (m) cc_final: 0.7816 (p) REVERT: I 214 LYS cc_start: 0.8393 (mttt) cc_final: 0.7848 (tptt) REVERT: L 79 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7313 (mt-10) REVERT: L 82 ASP cc_start: 0.8829 (m-30) cc_final: 0.8430 (m-30) REVERT: L 118 PHE cc_start: 0.8565 (m-80) cc_final: 0.7774 (m-80) REVERT: L 124 GLN cc_start: 0.7858 (tt0) cc_final: 0.7136 (tt0) REVERT: M 24 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8072 (ttp80) REVERT: M 79 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7289 (mt-10) REVERT: M 82 ASP cc_start: 0.8801 (m-30) cc_final: 0.8442 (m-30) REVERT: M 118 PHE cc_start: 0.8372 (m-80) cc_final: 0.7603 (m-80) REVERT: M 124 GLN cc_start: 0.7617 (tt0) cc_final: 0.7047 (tt0) REVERT: M 158 ASN cc_start: 0.7718 (t160) cc_final: 0.6768 (p0) outliers start: 42 outliers final: 32 residues processed: 228 average time/residue: 0.0849 time to fit residues: 28.1875 Evaluate side-chains 223 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 1 GLN M 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.159336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109234 restraints weight = 15886.277| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.48 r_work: 0.3194 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9593 Z= 0.129 Angle : 0.574 10.359 13080 Z= 0.288 Chirality : 0.041 0.158 1490 Planarity : 0.004 0.045 1608 Dihedral : 5.707 58.006 1362 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.22 % Allowed : 17.09 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.24), residues: 1192 helix: 1.85 (0.34), residues: 242 sheet: 1.75 (0.25), residues: 396 loop : 0.04 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 211 TYR 0.047 0.002 TYR C 94 PHE 0.013 0.001 PHE D 62 TRP 0.019 0.001 TRP D 89 HIS 0.002 0.000 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9582) covalent geometry : angle 0.57315 / 0.29 (13058) SS BOND : bond 0.00441 / 0.29 ( 11) SS BOND : angle 1.05553 / 0.63 ( 22) hydrogen bonds : bond 0.03653 / 2.48 ( 434) hydrogen bonds : angle 4.57423 / 3.22 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.7235 (p90) REVERT: C 116 LYS cc_start: 0.8594 (mttt) cc_final: 0.8219 (mmmt) REVERT: C 204 GLN cc_start: 0.9011 (tp40) cc_final: 0.8686 (tp-100) REVERT: D 116 LYS cc_start: 0.8358 (mttt) cc_final: 0.7847 (mttt) REVERT: H 5 GLN cc_start: 0.8562 (tt0) cc_final: 0.8147 (tp40) REVERT: H 64 LYS cc_start: 0.8978 (tttt) cc_final: 0.8521 (ttpp) REVERT: H 72 ASP cc_start: 0.8175 (t0) cc_final: 0.7616 (t0) REVERT: H 77 THR cc_start: 0.8988 (m) cc_final: 0.8465 (p) REVERT: H 85 GLU cc_start: 0.9109 (tp30) cc_final: 0.8879 (tp30) REVERT: H 86 ASP cc_start: 0.8360 (m-30) cc_final: 0.7906 (m-30) REVERT: H 154 TRP cc_start: 0.8461 (m100) cc_final: 0.8188 (m100) REVERT: H 161 SER cc_start: 0.8047 (m) cc_final: 0.7738 (p) REVERT: H 199 ASN cc_start: 0.7178 (t0) cc_final: 0.6973 (t0) REVERT: I 64 LYS cc_start: 0.8940 (tttt) cc_final: 0.8500 (ttpp) REVERT: I 72 ASP cc_start: 0.8228 (t0) cc_final: 0.7662 (t0) REVERT: I 77 THR cc_start: 0.8997 (m) cc_final: 0.8441 (p) REVERT: I 86 ASP cc_start: 0.8222 (m-30) cc_final: 0.7765 (m-30) REVERT: I 97 TYR cc_start: 0.8971 (t80) cc_final: 0.8547 (t80) REVERT: I 154 TRP cc_start: 0.8361 (m100) cc_final: 0.7964 (m100) REVERT: I 161 SER cc_start: 0.8150 (m) cc_final: 0.7815 (p) REVERT: I 214 LYS cc_start: 0.8462 (mttt) cc_final: 0.7942 (tptt) REVERT: L 24 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7818 (ttp80) REVERT: L 79 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7370 (mt-10) REVERT: L 82 ASP cc_start: 0.8824 (m-30) cc_final: 0.8468 (m-30) REVERT: L 118 PHE cc_start: 0.8553 (m-80) cc_final: 0.7824 (m-80) REVERT: L 124 GLN cc_start: 0.7831 (tt0) cc_final: 0.7121 (tt0) REVERT: M 24 ARG cc_start: 0.8414 (ttm110) cc_final: 0.8092 (ttp80) REVERT: M 79 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7379 (mt-10) REVERT: M 82 ASP cc_start: 0.8819 (m-30) cc_final: 0.8424 (m-30) REVERT: M 118 PHE cc_start: 0.8456 (m-80) cc_final: 0.7792 (m-80) REVERT: M 124 GLN cc_start: 0.7434 (tt0) cc_final: 0.6976 (tt0) REVERT: M 158 ASN cc_start: 0.7831 (t0) cc_final: 0.7619 (t0) outliers start: 33 outliers final: 26 residues processed: 225 average time/residue: 0.0853 time to fit residues: 28.0156 Evaluate side-chains 221 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 0.0470 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.157373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106352 restraints weight = 16220.954| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.54 r_work: 0.3140 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9593 Z= 0.180 Angle : 0.613 10.287 13080 Z= 0.309 Chirality : 0.042 0.155 1490 Planarity : 0.005 0.057 1608 Dihedral : 5.847 59.517 1362 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.61 % Allowed : 17.29 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1192 helix: 1.70 (0.34), residues: 242 sheet: 1.72 (0.26), residues: 384 loop : 0.04 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 109 TYR 0.044 0.002 TYR C 94 PHE 0.023 0.002 PHE D 62 TRP 0.019 0.002 TRP D 89 HIS 0.002 0.001 HIS M 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 9582) covalent geometry : angle 0.61177 / 0.31 (13058) SS BOND : bond 0.00495 / 0.34 ( 11) SS BOND : angle 1.27477 / 0.76 ( 22) hydrogen bonds : bond 0.04094 / 2.78 ( 434) hydrogen bonds : angle 4.75274 / 3.36 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8628 (OUTLIER) cc_final: 0.7292 (p90) REVERT: C 116 LYS cc_start: 0.8690 (mttt) cc_final: 0.8473 (mmmt) REVERT: C 197 MET cc_start: 0.9626 (ttm) cc_final: 0.9378 (ttp) REVERT: C 204 GLN cc_start: 0.9038 (tp40) cc_final: 0.8677 (tp-100) REVERT: D 116 LYS cc_start: 0.8480 (mttt) cc_final: 0.7991 (mttt) REVERT: D 197 MET cc_start: 0.9588 (ttm) cc_final: 0.9345 (ttp) REVERT: H 5 GLN cc_start: 0.8587 (tt0) cc_final: 0.8158 (tp40) REVERT: H 64 LYS cc_start: 0.9063 (tttt) cc_final: 0.8600 (ttpp) REVERT: H 72 ASP cc_start: 0.8188 (t0) cc_final: 0.7613 (t0) REVERT: H 77 THR cc_start: 0.8984 (m) cc_final: 0.8382 (p) REVERT: H 85 GLU cc_start: 0.9118 (tp30) cc_final: 0.8890 (tp30) REVERT: H 86 ASP cc_start: 0.8392 (m-30) cc_final: 0.7944 (m-30) REVERT: H 154 TRP cc_start: 0.8437 (m100) cc_final: 0.8150 (m100) REVERT: H 161 SER cc_start: 0.8074 (m) cc_final: 0.7737 (p) REVERT: H 199 ASN cc_start: 0.7070 (t0) cc_final: 0.6852 (t0) REVERT: I 64 LYS cc_start: 0.9005 (tttt) cc_final: 0.8579 (ttpp) REVERT: I 72 ASP cc_start: 0.8241 (t0) cc_final: 0.7663 (t0) REVERT: I 77 THR cc_start: 0.8995 (m) cc_final: 0.8352 (p) REVERT: I 86 ASP cc_start: 0.8284 (m-30) cc_final: 0.7829 (m-30) REVERT: I 97 TYR cc_start: 0.9044 (t80) cc_final: 0.8686 (t80) REVERT: I 154 TRP cc_start: 0.8354 (m100) cc_final: 0.7922 (m100) REVERT: I 161 SER cc_start: 0.8210 (m) cc_final: 0.7903 (p) REVERT: I 214 LYS cc_start: 0.8399 (mttt) cc_final: 0.7852 (tptt) REVERT: L 24 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7858 (ttp80) REVERT: L 79 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7422 (mt-10) REVERT: L 82 ASP cc_start: 0.8853 (m-30) cc_final: 0.8400 (m-30) REVERT: L 118 PHE cc_start: 0.8589 (m-80) cc_final: 0.7836 (m-80) REVERT: L 124 GLN cc_start: 0.7739 (tt0) cc_final: 0.7029 (tt0) REVERT: L 211 ARG cc_start: 0.7158 (ptm-80) cc_final: 0.6826 (ptm-80) REVERT: M 24 ARG cc_start: 0.8380 (ttm110) cc_final: 0.8031 (ttp80) REVERT: M 79 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7391 (mt-10) REVERT: M 82 ASP cc_start: 0.8838 (m-30) cc_final: 0.8413 (m-30) REVERT: M 118 PHE cc_start: 0.8360 (m-80) cc_final: 0.7691 (m-80) REVERT: M 124 GLN cc_start: 0.7364 (tt0) cc_final: 0.6882 (tt0) REVERT: M 158 ASN cc_start: 0.7729 (t0) cc_final: 0.7522 (t0) outliers start: 37 outliers final: 28 residues processed: 212 average time/residue: 0.0832 time to fit residues: 25.9465 Evaluate side-chains 214 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 52 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.158444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107778 restraints weight = 15943.615| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.49 r_work: 0.3155 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9593 Z= 0.147 Angle : 0.602 12.229 13080 Z= 0.298 Chirality : 0.042 0.152 1490 Planarity : 0.005 0.046 1608 Dihedral : 5.771 56.253 1362 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.91 % Allowed : 16.99 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1192 helix: 1.78 (0.34), residues: 242 sheet: 1.75 (0.25), residues: 394 loop : 0.00 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 109 TYR 0.039 0.002 TYR C 94 PHE 0.017 0.001 PHE D 62 TRP 0.019 0.001 TRP D 89 HIS 0.002 0.000 HIS M 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9582) covalent geometry : angle 0.60074 / 0.30 (13058) SS BOND : bond 0.00454 / 0.30 ( 11) SS BOND : angle 1.14255 / 0.67 ( 22) hydrogen bonds : bond 0.03807 / 2.60 ( 434) hydrogen bonds : angle 4.63621 / 3.27 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8604 (OUTLIER) cc_final: 0.7216 (p90) REVERT: C 116 LYS cc_start: 0.8663 (mttt) cc_final: 0.8436 (mmmt) REVERT: C 204 GLN cc_start: 0.8992 (tp40) cc_final: 0.8600 (tp-100) REVERT: D 116 LYS cc_start: 0.8441 (mttt) cc_final: 0.7930 (mttt) REVERT: D 197 MET cc_start: 0.9576 (ttm) cc_final: 0.9316 (ttp) REVERT: H 5 GLN cc_start: 0.8570 (tt0) cc_final: 0.8140 (tp40) REVERT: H 64 LYS cc_start: 0.8998 (tttt) cc_final: 0.8542 (ttpp) REVERT: H 72 ASP cc_start: 0.8172 (t0) cc_final: 0.7594 (t0) REVERT: H 77 THR cc_start: 0.8981 (m) cc_final: 0.8392 (p) REVERT: H 85 GLU cc_start: 0.9109 (tp30) cc_final: 0.8880 (tp30) REVERT: H 86 ASP cc_start: 0.8353 (m-30) cc_final: 0.7879 (m-30) REVERT: H 154 TRP cc_start: 0.8444 (m100) cc_final: 0.8166 (m100) REVERT: H 161 SER cc_start: 0.8065 (m) cc_final: 0.7812 (p) REVERT: H 199 ASN cc_start: 0.7094 (t0) cc_final: 0.6874 (t0) REVERT: I 64 LYS cc_start: 0.8958 (tttt) cc_final: 0.8537 (ttpp) REVERT: I 72 ASP cc_start: 0.8214 (t0) cc_final: 0.7636 (t0) REVERT: I 77 THR cc_start: 0.8985 (m) cc_final: 0.8386 (p) REVERT: I 86 ASP cc_start: 0.8227 (m-30) cc_final: 0.7802 (m-30) REVERT: I 97 TYR cc_start: 0.9007 (t80) cc_final: 0.8636 (t80) REVERT: I 154 TRP cc_start: 0.8392 (m100) cc_final: 0.7919 (m100) REVERT: I 161 SER cc_start: 0.8212 (m) cc_final: 0.7908 (p) REVERT: I 214 LYS cc_start: 0.8437 (mttt) cc_final: 0.7937 (tptt) REVERT: L 24 ARG cc_start: 0.8172 (ttp-110) cc_final: 0.7853 (ttp80) REVERT: L 79 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7397 (mt-10) REVERT: L 82 ASP cc_start: 0.8846 (m-30) cc_final: 0.8424 (m-30) REVERT: L 118 PHE cc_start: 0.8581 (m-80) cc_final: 0.7826 (m-80) REVERT: L 124 GLN cc_start: 0.7748 (tt0) cc_final: 0.7062 (tt0) REVERT: L 211 ARG cc_start: 0.7118 (ptm-80) cc_final: 0.6703 (ptm-80) REVERT: M 24 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8028 (ttp80) REVERT: M 79 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7470 (mt-10) REVERT: M 82 ASP cc_start: 0.8828 (m-30) cc_final: 0.8415 (m-30) REVERT: M 118 PHE cc_start: 0.8341 (m-80) cc_final: 0.7695 (m-80) REVERT: M 124 GLN cc_start: 0.7396 (tt0) cc_final: 0.6911 (tt0) outliers start: 40 outliers final: 31 residues processed: 215 average time/residue: 0.0833 time to fit residues: 26.4774 Evaluate side-chains 216 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 21 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 73 optimal weight: 0.0270 chunk 35 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN M 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.160596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111149 restraints weight = 15935.453| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.53 r_work: 0.3216 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9593 Z= 0.094 Angle : 0.566 12.365 13080 Z= 0.278 Chirality : 0.041 0.149 1490 Planarity : 0.004 0.044 1608 Dihedral : 5.381 53.024 1362 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.44 % Allowed : 18.65 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.25), residues: 1192 helix: 1.82 (0.34), residues: 250 sheet: 1.91 (0.25), residues: 388 loop : 0.16 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 211 TYR 0.040 0.001 TYR C 94 PHE 0.010 0.001 PHE I 122 TRP 0.019 0.001 TRP D 89 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 9582) covalent geometry : angle 0.56471 / 0.28 (13058) SS BOND : bond 0.00374 / 0.25 ( 11) SS BOND : angle 0.96053 / 0.67 ( 22) hydrogen bonds : bond 0.03069 / 2.06 ( 434) hydrogen bonds : angle 4.29446 / 3.01 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8407 (OUTLIER) cc_final: 0.7161 (p90) REVERT: C 94 TYR cc_start: 0.9311 (m-80) cc_final: 0.9107 (m-80) REVERT: C 116 LYS cc_start: 0.8552 (mttt) cc_final: 0.8208 (mmmt) REVERT: D 89 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7328 (p90) REVERT: D 116 LYS cc_start: 0.8363 (mttt) cc_final: 0.7843 (mttt) REVERT: D 204 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8828 (tm-30) REVERT: H 5 GLN cc_start: 0.8573 (tt0) cc_final: 0.8189 (tp40) REVERT: H 64 LYS cc_start: 0.8813 (tttt) cc_final: 0.8380 (ttpp) REVERT: H 72 ASP cc_start: 0.8066 (t0) cc_final: 0.7481 (t0) REVERT: H 77 THR cc_start: 0.8932 (m) cc_final: 0.8460 (p) REVERT: H 85 GLU cc_start: 0.9090 (tp30) cc_final: 0.8854 (tp30) REVERT: H 86 ASP cc_start: 0.8304 (m-30) cc_final: 0.7830 (m-30) REVERT: H 161 SER cc_start: 0.8141 (m) cc_final: 0.7801 (p) REVERT: I 64 LYS cc_start: 0.8752 (tttt) cc_final: 0.8353 (ttpp) REVERT: I 72 ASP cc_start: 0.8097 (t0) cc_final: 0.7495 (t0) REVERT: I 77 THR cc_start: 0.8939 (m) cc_final: 0.8448 (p) REVERT: I 97 TYR cc_start: 0.8831 (t80) cc_final: 0.8554 (t80) REVERT: I 154 TRP cc_start: 0.8279 (m100) cc_final: 0.8027 (m100) REVERT: I 161 SER cc_start: 0.8173 (m) cc_final: 0.7871 (p) REVERT: I 214 LYS cc_start: 0.8465 (mttt) cc_final: 0.7965 (tptt) REVERT: L 24 ARG cc_start: 0.8051 (ttp-110) cc_final: 0.7758 (ttp80) REVERT: L 79 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7304 (mt-10) REVERT: L 82 ASP cc_start: 0.8816 (m-30) cc_final: 0.8463 (m-30) REVERT: L 118 PHE cc_start: 0.8545 (m-80) cc_final: 0.8026 (m-80) REVERT: L 124 GLN cc_start: 0.7785 (tt0) cc_final: 0.7092 (tt0) REVERT: L 211 ARG cc_start: 0.7185 (ptm-80) cc_final: 0.6811 (ptm-80) REVERT: M 24 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8043 (ttp80) REVERT: M 79 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7386 (mt-10) REVERT: M 82 ASP cc_start: 0.8781 (m-30) cc_final: 0.8440 (m-30) REVERT: M 118 PHE cc_start: 0.8359 (m-80) cc_final: 0.7758 (m-80) REVERT: M 124 GLN cc_start: 0.7487 (tt0) cc_final: 0.6997 (tt0) REVERT: M 158 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.5943 (p0) REVERT: M 167 ASP cc_start: 0.7597 (t70) cc_final: 0.7309 (t0) outliers start: 25 outliers final: 19 residues processed: 227 average time/residue: 0.0800 time to fit residues: 26.8767 Evaluate side-chains 219 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 0.0370 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.159581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109793 restraints weight = 15950.663| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.57 r_work: 0.3219 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9593 Z= 0.112 Angle : 0.607 13.331 13080 Z= 0.293 Chirality : 0.041 0.151 1490 Planarity : 0.005 0.046 1608 Dihedral : 5.405 51.319 1362 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.44 % Allowed : 19.24 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.25), residues: 1192 helix: 1.77 (0.34), residues: 250 sheet: 1.89 (0.25), residues: 386 loop : 0.22 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 211 TYR 0.040 0.001 TYR C 94 PHE 0.013 0.001 PHE D 62 TRP 0.046 0.002 TRP H 154 HIS 0.001 0.000 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9582) covalent geometry : angle 0.60577 / 0.29 (13058) SS BOND : bond 0.00365 / 0.24 ( 11) SS BOND : angle 1.05111 / 0.62 ( 22) hydrogen bonds : bond 0.03227 / 2.18 ( 434) hydrogen bonds : angle 4.35616 / 3.06 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8381 (OUTLIER) cc_final: 0.7119 (p90) REVERT: C 116 LYS cc_start: 0.8570 (mttt) cc_final: 0.8233 (mmmt) REVERT: C 197 MET cc_start: 0.9624 (ttm) cc_final: 0.9390 (ttp) REVERT: D 89 TRP cc_start: 0.8538 (OUTLIER) cc_final: 0.7446 (p90) REVERT: D 116 LYS cc_start: 0.8369 (mttt) cc_final: 0.7887 (mttt) REVERT: D 197 MET cc_start: 0.9584 (ttm) cc_final: 0.9296 (ttp) REVERT: D 204 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8846 (tm-30) REVERT: H 5 GLN cc_start: 0.8580 (tt0) cc_final: 0.8205 (tp40) REVERT: H 64 LYS cc_start: 0.8838 (tttt) cc_final: 0.8393 (ttpp) REVERT: H 77 THR cc_start: 0.8966 (m) cc_final: 0.8509 (p) REVERT: H 85 GLU cc_start: 0.9071 (tp30) cc_final: 0.8851 (tp30) REVERT: H 86 ASP cc_start: 0.8333 (m-30) cc_final: 0.7867 (m-30) REVERT: H 161 SER cc_start: 0.8195 (m) cc_final: 0.7879 (p) REVERT: I 64 LYS cc_start: 0.8792 (tttt) cc_final: 0.8391 (ttpp) REVERT: I 77 THR cc_start: 0.8977 (m) cc_final: 0.8505 (p) REVERT: I 97 TYR cc_start: 0.8926 (t80) cc_final: 0.8524 (t80) REVERT: I 154 TRP cc_start: 0.8274 (m100) cc_final: 0.8000 (m100) REVERT: I 161 SER cc_start: 0.8271 (m) cc_final: 0.7964 (p) REVERT: I 214 LYS cc_start: 0.8497 (mttt) cc_final: 0.8020 (tptt) REVERT: L 79 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7351 (mt-10) REVERT: L 82 ASP cc_start: 0.8777 (m-30) cc_final: 0.8447 (m-30) REVERT: L 118 PHE cc_start: 0.8547 (m-80) cc_final: 0.8053 (m-80) REVERT: L 124 GLN cc_start: 0.7741 (tt0) cc_final: 0.7019 (tt0) REVERT: L 211 ARG cc_start: 0.7155 (ptm-80) cc_final: 0.6742 (ptm-80) REVERT: M 24 ARG cc_start: 0.8393 (ttm110) cc_final: 0.8077 (ttp80) REVERT: M 79 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7387 (mt-10) REVERT: M 82 ASP cc_start: 0.8738 (m-30) cc_final: 0.8426 (m-30) REVERT: M 118 PHE cc_start: 0.8371 (m-80) cc_final: 0.7787 (m-80) REVERT: M 124 GLN cc_start: 0.7423 (tt0) cc_final: 0.6900 (tt0) REVERT: M 167 ASP cc_start: 0.7630 (t70) cc_final: 0.7343 (t0) outliers start: 25 outliers final: 21 residues processed: 209 average time/residue: 0.0773 time to fit residues: 23.9308 Evaluate side-chains 210 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 47 optimal weight: 0.4980 chunk 109 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111793 restraints weight = 15691.426| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.47 r_work: 0.3248 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9593 Z= 0.102 Angle : 0.593 13.485 13080 Z= 0.285 Chirality : 0.041 0.154 1490 Planarity : 0.004 0.044 1608 Dihedral : 5.271 47.778 1362 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.44 % Allowed : 19.34 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1192 helix: 1.87 (0.34), residues: 248 sheet: 1.93 (0.25), residues: 392 loop : 0.24 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 211 TYR 0.021 0.001 TYR C 94 PHE 0.012 0.001 PHE C 203 TRP 0.033 0.002 TRP H 154 HIS 0.002 0.000 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 9582) covalent geometry : angle 0.59210 / 0.28 (13058) SS BOND : bond 0.00345 / 0.22 ( 11) SS BOND : angle 0.91426 / 0.54 ( 22) hydrogen bonds : bond 0.03071 / 2.06 ( 434) hydrogen bonds : angle 4.25162 / 2.99 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.20 seconds wall clock time: 42 minutes 16.46 seconds (2536.46 seconds total)