Starting phenix.real_space_refine on Wed Mar 4 00:33:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vja_21212/03_2026/6vja_21212.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vja_21212/03_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_21212/03_2026/6vja_21212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vja_21212/03_2026/6vja_21212.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vja_21212/03_2026/6vja_21212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vja_21212/03_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-dev-5986/lib/python3.9/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: 2.27, per 1000 atoms: 0.24 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: 0.81 Conformation dependent library (CDL) restraints added in 314.3 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: 0.38 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: 1.62 Time building geometry restraints manager: 0.96 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: 5658 17.90 - 35.80: 272 35.80 - 53.70: 51 53.70 - 71.60: 30 71.60 - 89.49: 12 Dihedral angle restraints: 6023 sinusoidal: 2543 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 6020 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: 0.00 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: 2.920 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.090 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 12.613 89.494 3766 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 covalent geometry : bond 0.01370 ( 9582) covalent geometry : angle 1.27006 (13058) SS BOND : bond 0.01058 ( 11) SS BOND : angle 2.51481 ( 22) hydrogen bonds : bond 0.21402 ( 434) hydrogen bonds : angle 8.48481 ( 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 : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.0863 time to fit residues: 37.1269 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 : 0.318 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4001 r_free = 0.4001 target = 0.159260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110110 restraints weight = 15963.775| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.51 r_work: 0.3220 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9593 Z= 0.128 Angle : 0.655 8.829 13080 Z= 0.332 Chirality : 0.044 0.208 1490 Planarity : 0.004 0.044 1608 Dihedral : 7.679 59.376 1710 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.86 % Allowed : 11.04 % 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: 1.68 (0.25), residues: 1192 helix: 1.03 (0.33), residues: 248 sheet: 2.17 (0.25), residues: 404 loop : 0.40 (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 0.015 0.001 PHE I 122 TRP 0.021 0.002 TRP D 89 HIS 0.004 0.001 HIS D 145 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9582) covalent geometry : angle 0.65212 (13058) SS BOND : bond 0.00666 ( 11) SS BOND : angle 1.53253 ( 22) hydrogen bonds : bond 0.04636 ( 434) hydrogen bonds : angle 5.39603 ( 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 282 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 TYR cc_start: 0.7205 (m-10) cc_final: 0.6950 (m-10) REVERT: C 116 LYS cc_start: 0.8525 (mttt) cc_final: 0.8104 (mmmt) REVERT: C 139 LEU cc_start: 0.9004 (mm) cc_final: 0.8713 (mm) REVERT: C 148 LYS cc_start: 0.6794 (pttp) cc_final: 0.6527 (ptmt) REVERT: C 175 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8251 (mmtp) REVERT: D 62 PHE cc_start: 0.8714 (t80) cc_final: 0.8379 (t80) REVERT: D 89 TRP cc_start: 0.8737 (OUTLIER) cc_final: 0.7628 (p90) REVERT: D 116 LYS cc_start: 0.8198 (mttt) cc_final: 0.7642 (mttt) REVERT: D 175 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8361 (mmtp) REVERT: H 5 GLN cc_start: 0.8614 (tt0) cc_final: 0.8193 (tp40) REVERT: H 64 LYS cc_start: 0.8703 (tttt) cc_final: 0.8290 (ttpp) REVERT: H 72 ASP cc_start: 0.8218 (t0) cc_final: 0.7700 (t0) REVERT: H 77 THR cc_start: 0.8921 (m) cc_final: 0.8316 (p) REVERT: H 86 ASP cc_start: 0.8424 (m-30) cc_final: 0.8151 (m-30) REVERT: H 154 TRP cc_start: 0.8124 (m100) cc_final: 0.7716 (m100) REVERT: I 5 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7645 (mp10) REVERT: I 64 LYS cc_start: 0.8832 (tttt) cc_final: 0.8412 (ttpp) REVERT: I 72 ASP cc_start: 0.8134 (t0) cc_final: 0.7689 (t0) REVERT: I 77 THR cc_start: 0.8922 (m) cc_final: 0.8310 (p) REVERT: I 86 ASP cc_start: 0.8326 (m-30) cc_final: 0.7965 (m-30) REVERT: I 122 PHE cc_start: 0.7203 (m-10) cc_final: 0.6935 (m-10) REVERT: I 154 TRP cc_start: 0.8114 (m100) cc_final: 0.7705 (m100) REVERT: I 161 SER cc_start: 0.8143 (m) cc_final: 0.7737 (p) REVERT: I 214 LYS cc_start: 0.8472 (mttt) cc_final: 0.7974 (tptt) REVERT: L 24 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7884 (ttp80) REVERT: L 79 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7093 (mt-10) REVERT: L 82 ASP cc_start: 0.8786 (m-30) cc_final: 0.8450 (m-30) REVERT: L 118 PHE cc_start: 0.8632 (m-80) cc_final: 0.7786 (m-80) REVERT: L 124 GLN cc_start: 0.7947 (tt0) cc_final: 0.7393 (tt0) REVERT: M 24 ARG cc_start: 0.8430 (ttm110) cc_final: 0.8127 (ttp80) REVERT: M 79 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7199 (mt-10) REVERT: M 82 ASP cc_start: 0.8797 (m-30) cc_final: 0.8466 (m-30) REVERT: M 118 PHE cc_start: 0.8559 (m-80) cc_final: 0.7780 (m-80) REVERT: M 124 GLN cc_start: 0.7829 (tt0) cc_final: 0.7406 (tt0) outliers start: 19 outliers final: 9 residues processed: 274 average time/residue: 0.0764 time to fit residues: 30.0319 Evaluate side-chains 227 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP 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: 8.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 106 optimal weight: 0.0570 chunk 92 optimal weight: 7.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3989 r_free = 0.3989 target = 0.159154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109107 restraints weight = 15799.013| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.46 r_work: 0.3202 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9593 Z= 0.140 Angle : 0.620 8.016 13080 Z= 0.312 Chirality : 0.043 0.180 1490 Planarity : 0.005 0.048 1608 Dihedral : 7.361 55.885 1710 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.71 % Allowed : 12.40 % Favored : 83.89 % 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: 1.75 (0.25), residues: 1192 helix: 1.43 (0.34), residues: 246 sheet: 2.11 (0.26), residues: 372 loop : 0.48 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 211 TYR 0.043 0.002 TYR D 94 PHE 0.013 0.001 PHE H 100D TRP 0.018 0.001 TRP D 89 HIS 0.004 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9582) covalent geometry : angle 0.61230 (13058) SS BOND : bond 0.00583 ( 11) SS BOND : angle 2.49706 ( 22) hydrogen bonds : bond 0.04048 ( 434) hydrogen bonds : angle 4.85084 ( 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 268 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8688 (OUTLIER) cc_final: 0.7437 (p90) REVERT: C 116 LYS cc_start: 0.8485 (mttt) cc_final: 0.8151 (mmmt) REVERT: D 62 PHE cc_start: 0.8621 (t80) cc_final: 0.8236 (t80) REVERT: D 89 TRP cc_start: 0.8679 (OUTLIER) cc_final: 0.7494 (p90) REVERT: D 116 LYS cc_start: 0.8362 (mttt) cc_final: 0.7814 (mttt) REVERT: H 5 GLN cc_start: 0.8595 (tt0) cc_final: 0.8183 (tp40) REVERT: H 64 LYS cc_start: 0.8904 (tttt) cc_final: 0.8483 (ttpp) REVERT: H 72 ASP cc_start: 0.8281 (t0) cc_final: 0.7736 (t0) REVERT: H 77 THR cc_start: 0.8966 (m) cc_final: 0.8417 (p) REVERT: H 85 GLU cc_start: 0.9132 (tp30) cc_final: 0.8867 (tp30) REVERT: H 86 ASP cc_start: 0.8400 (m-30) cc_final: 0.8019 (m-30) REVERT: H 154 TRP cc_start: 0.8332 (m100) cc_final: 0.7986 (m100) REVERT: I 64 LYS cc_start: 0.8962 (tttt) cc_final: 0.8526 (ttpp) REVERT: I 72 ASP cc_start: 0.8358 (t0) cc_final: 0.7853 (t0) REVERT: I 77 THR cc_start: 0.8957 (m) cc_final: 0.8372 (p) REVERT: I 86 ASP cc_start: 0.8340 (m-30) cc_final: 0.7879 (m-30) REVERT: I 97 TYR cc_start: 0.8987 (t80) cc_final: 0.8658 (t80) REVERT: I 154 TRP cc_start: 0.8250 (m100) cc_final: 0.7877 (m100) REVERT: I 161 SER cc_start: 0.8186 (m) cc_final: 0.7854 (p) REVERT: I 214 LYS cc_start: 0.8485 (mttt) cc_final: 0.7939 (tptt) REVERT: L 79 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7156 (mt-10) REVERT: L 82 ASP cc_start: 0.8772 (m-30) cc_final: 0.8426 (m-30) REVERT: L 118 PHE cc_start: 0.8568 (m-80) cc_final: 0.7844 (m-80) REVERT: L 124 GLN cc_start: 0.7889 (tt0) cc_final: 0.7148 (tt0) REVERT: M 24 ARG cc_start: 0.8440 (ttm110) cc_final: 0.8122 (ttp80) REVERT: M 79 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7215 (mt-10) REVERT: M 82 ASP cc_start: 0.8767 (m-30) cc_final: 0.8434 (m-30) REVERT: M 118 PHE cc_start: 0.8554 (m-80) cc_final: 0.7870 (m-80) REVERT: M 124 GLN cc_start: 0.7883 (tt0) cc_final: 0.7431 (tt0) REVERT: M 126 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7888 (tppt) outliers start: 38 outliers final: 29 residues processed: 253 average time/residue: 0.0738 time to fit residues: 27.4156 Evaluate side-chains 244 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 142 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 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 178 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 214 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.160379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.110197 restraints weight = 16023.191| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.51 r_work: 0.3165 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9593 Z= 0.116 Angle : 0.573 7.304 13080 Z= 0.286 Chirality : 0.042 0.162 1490 Planarity : 0.004 0.046 1608 Dihedral : 7.168 55.151 1710 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.32 % Allowed : 14.84 % Favored : 81.84 % 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: 1.83 (0.25), residues: 1192 helix: 1.69 (0.34), residues: 246 sheet: 2.10 (0.25), residues: 382 loop : 0.43 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 211 TYR 0.045 0.002 TYR D 94 PHE 0.013 0.001 PHE C 62 TRP 0.019 0.001 TRP D 89 HIS 0.002 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9582) covalent geometry : angle 0.57073 (13058) SS BOND : bond 0.00462 ( 11) SS BOND : angle 1.45374 ( 22) hydrogen bonds : bond 0.03563 ( 434) hydrogen bonds : angle 4.58605 ( 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 252 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.7355 (p90) REVERT: C 116 LYS cc_start: 0.8513 (mttt) cc_final: 0.8170 (mmmt) REVERT: D 116 LYS cc_start: 0.8337 (mttt) cc_final: 0.7780 (mttt) REVERT: H 5 GLN cc_start: 0.8575 (tt0) cc_final: 0.8198 (tp40) REVERT: H 64 LYS cc_start: 0.8882 (tttt) cc_final: 0.8463 (ttpp) REVERT: H 72 ASP cc_start: 0.8156 (t0) cc_final: 0.7574 (t0) REVERT: H 77 THR cc_start: 0.8936 (m) cc_final: 0.8388 (p) REVERT: H 85 GLU cc_start: 0.9134 (tp30) cc_final: 0.8873 (tp30) REVERT: H 86 ASP cc_start: 0.8332 (m-30) cc_final: 0.7930 (m-30) REVERT: H 161 SER cc_start: 0.8094 (m) cc_final: 0.7729 (p) REVERT: I 64 LYS cc_start: 0.8909 (tttt) cc_final: 0.8470 (ttpp) REVERT: I 72 ASP cc_start: 0.8193 (t0) cc_final: 0.7619 (t0) REVERT: I 77 THR cc_start: 0.8933 (m) cc_final: 0.8369 (p) REVERT: I 86 ASP cc_start: 0.8244 (m-30) cc_final: 0.7816 (m-30) REVERT: I 97 TYR cc_start: 0.8956 (t80) cc_final: 0.8552 (t80) REVERT: I 154 TRP cc_start: 0.8261 (m100) cc_final: 0.7918 (m100) REVERT: I 161 SER cc_start: 0.8131 (m) cc_final: 0.7815 (p) REVERT: I 214 LYS cc_start: 0.8479 (mttt) cc_final: 0.7965 (tptt) REVERT: L 79 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7222 (mt-10) REVERT: L 82 ASP cc_start: 0.8762 (m-30) cc_final: 0.8363 (m-30) REVERT: L 118 PHE cc_start: 0.8547 (m-80) cc_final: 0.7862 (m-80) REVERT: L 124 GLN cc_start: 0.7807 (tt0) cc_final: 0.7078 (tt0) REVERT: M 24 ARG cc_start: 0.8418 (ttm110) cc_final: 0.8103 (ttp80) REVERT: M 79 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7223 (mt-10) REVERT: M 82 ASP cc_start: 0.8797 (m-30) cc_final: 0.8463 (m-30) REVERT: M 118 PHE cc_start: 0.8556 (m-80) cc_final: 0.7887 (m-80) REVERT: M 124 GLN cc_start: 0.7642 (tt0) cc_final: 0.7183 (tt0) REVERT: M 126 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7900 (tppt) REVERT: M 213 GLU cc_start: 0.7524 (pp20) cc_final: 0.7096 (pp20) outliers start: 34 outliers final: 25 residues processed: 240 average time/residue: 0.0774 time to fit residues: 26.9955 Evaluate side-chains 233 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 138 ILE Chi-restraints excluded: chain C residue 149 MET 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 H residue 12 VAL Chi-restraints excluded: chain H residue 128 SER 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 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 I residue 197 ASN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 176 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 81 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 27 optimal weight: 0.0030 chunk 61 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110516 restraints weight = 15909.947| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.51 r_work: 0.3220 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9593 Z= 0.112 Angle : 0.570 8.374 13080 Z= 0.282 Chirality : 0.041 0.167 1490 Planarity : 0.004 0.047 1608 Dihedral : 7.013 56.483 1710 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.52 % Allowed : 15.82 % 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: 1.93 (0.25), residues: 1192 helix: 1.88 (0.34), residues: 242 sheet: 2.16 (0.25), residues: 390 loop : 0.41 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 211 TYR 0.048 0.002 TYR D 94 PHE 0.013 0.001 PHE D 62 TRP 0.019 0.001 TRP D 89 HIS 0.002 0.000 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9582) covalent geometry : angle 0.56595 (13058) SS BOND : bond 0.00458 ( 11) SS BOND : angle 1.77969 ( 22) hydrogen bonds : bond 0.03399 ( 434) hydrogen bonds : angle 4.47848 ( 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 246 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.7270 (p90) REVERT: C 116 LYS cc_start: 0.8539 (mttt) cc_final: 0.8216 (mmmt) REVERT: C 175 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8321 (mmtp) REVERT: D 89 TRP cc_start: 0.8546 (OUTLIER) cc_final: 0.7187 (p90) REVERT: D 116 LYS cc_start: 0.8313 (mttt) cc_final: 0.7785 (mttt) REVERT: D 166 ASN cc_start: 0.8122 (t0) cc_final: 0.7912 (t0) REVERT: D 175 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8363 (mmtp) REVERT: H 5 GLN cc_start: 0.8588 (tt0) cc_final: 0.8227 (tp40) REVERT: H 64 LYS cc_start: 0.8886 (tttt) cc_final: 0.8482 (ttpp) REVERT: H 72 ASP cc_start: 0.8169 (t0) cc_final: 0.7550 (t0) REVERT: H 77 THR cc_start: 0.8942 (m) cc_final: 0.8434 (p) REVERT: H 85 GLU cc_start: 0.9086 (tp30) cc_final: 0.8849 (tp30) REVERT: H 86 ASP cc_start: 0.8324 (m-30) cc_final: 0.7873 (m-30) REVERT: H 154 TRP cc_start: 0.8289 (m100) cc_final: 0.8020 (m100) REVERT: H 161 SER cc_start: 0.8062 (m) cc_final: 0.7715 (p) REVERT: I 64 LYS cc_start: 0.8885 (tttt) cc_final: 0.8451 (ttpp) REVERT: I 72 ASP cc_start: 0.8215 (t0) cc_final: 0.7603 (t0) REVERT: I 77 THR cc_start: 0.8957 (m) cc_final: 0.8439 (p) REVERT: I 97 TYR cc_start: 0.8905 (t80) cc_final: 0.8439 (t80) REVERT: I 154 TRP cc_start: 0.8353 (m100) cc_final: 0.8016 (m100) REVERT: I 161 SER cc_start: 0.8139 (m) cc_final: 0.7787 (p) REVERT: I 214 LYS cc_start: 0.8498 (mttt) cc_final: 0.7978 (tptt) REVERT: L 82 ASP cc_start: 0.8712 (m-30) cc_final: 0.8495 (m-30) REVERT: L 118 PHE cc_start: 0.8520 (m-80) cc_final: 0.7964 (m-80) REVERT: L 124 GLN cc_start: 0.7824 (tt0) cc_final: 0.7095 (tt0) REVERT: L 211 ARG cc_start: 0.7746 (ptm-80) cc_final: 0.7207 (ttm110) REVERT: M 24 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8098 (ttp80) REVERT: M 79 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7229 (mt-10) REVERT: M 82 ASP cc_start: 0.8752 (m-30) cc_final: 0.8382 (m-30) REVERT: M 118 PHE cc_start: 0.8593 (m-80) cc_final: 0.8040 (m-80) REVERT: M 124 GLN cc_start: 0.7563 (tt0) cc_final: 0.6914 (tt0) REVERT: M 126 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7732 (tppt) REVERT: M 148 TRP cc_start: 0.6914 (m100) cc_final: 0.6655 (m100) outliers start: 36 outliers final: 27 residues processed: 231 average time/residue: 0.0794 time to fit residues: 26.6713 Evaluate side-chains 228 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 138 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 149 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 128 SER 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 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 I residue 197 ASN Chi-restraints excluded: chain L residue 29 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109061 restraints weight = 16151.236| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.49 r_work: 0.3213 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9593 Z= 0.118 Angle : 0.568 11.672 13080 Z= 0.281 Chirality : 0.041 0.146 1490 Planarity : 0.004 0.046 1608 Dihedral : 6.949 59.965 1710 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.42 % Allowed : 16.70 % Favored : 79.88 % 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: 1.91 (0.25), residues: 1192 helix: 1.96 (0.34), residues: 242 sheet: 2.16 (0.25), residues: 390 loop : 0.34 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 211 TYR 0.040 0.002 TYR C 94 PHE 0.012 0.001 PHE I 122 TRP 0.019 0.001 TRP D 89 HIS 0.002 0.000 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9582) covalent geometry : angle 0.56497 (13058) SS BOND : bond 0.00435 ( 11) SS BOND : angle 1.49444 ( 22) hydrogen bonds : bond 0.03414 ( 434) hydrogen bonds : angle 4.44871 ( 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 241 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.7295 (p90) REVERT: C 116 LYS cc_start: 0.8549 (mttt) cc_final: 0.8211 (mmmt) REVERT: D 89 TRP cc_start: 0.8531 (OUTLIER) cc_final: 0.7166 (p90) REVERT: D 116 LYS cc_start: 0.8371 (mttt) cc_final: 0.7857 (mttt) REVERT: H 5 GLN cc_start: 0.8598 (tt0) cc_final: 0.8242 (tp40) REVERT: H 64 LYS cc_start: 0.8911 (tttt) cc_final: 0.8473 (ttpp) REVERT: H 72 ASP cc_start: 0.8163 (t0) cc_final: 0.7539 (t0) REVERT: H 77 THR cc_start: 0.8986 (m) cc_final: 0.8473 (p) REVERT: H 85 GLU cc_start: 0.9057 (tp30) cc_final: 0.8832 (tp30) REVERT: H 86 ASP cc_start: 0.8352 (m-30) cc_final: 0.7920 (m-30) REVERT: H 154 TRP cc_start: 0.8180 (m100) cc_final: 0.7935 (m100) REVERT: H 161 SER cc_start: 0.8061 (m) cc_final: 0.7739 (p) REVERT: H 210 LYS cc_start: 0.8295 (ptmt) cc_final: 0.7941 (ptmt) REVERT: H 212 GLU cc_start: 0.7910 (pm20) cc_final: 0.7683 (pm20) REVERT: I 64 LYS cc_start: 0.8911 (tttt) cc_final: 0.8482 (ttpp) REVERT: I 72 ASP cc_start: 0.8215 (t0) cc_final: 0.7615 (t0) REVERT: I 77 THR cc_start: 0.8997 (m) cc_final: 0.8489 (p) REVERT: I 85 GLU cc_start: 0.8987 (tp30) cc_final: 0.8780 (tp30) REVERT: I 97 TYR cc_start: 0.8926 (t80) cc_final: 0.8453 (t80) REVERT: I 154 TRP cc_start: 0.8340 (m100) cc_final: 0.8082 (m100) REVERT: I 161 SER cc_start: 0.8145 (m) cc_final: 0.7809 (p) REVERT: I 214 LYS cc_start: 0.8477 (mttt) cc_final: 0.7921 (tptt) REVERT: L 79 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7250 (mt-10) REVERT: L 82 ASP cc_start: 0.8756 (m-30) cc_final: 0.8398 (m-30) REVERT: L 118 PHE cc_start: 0.8534 (m-80) cc_final: 0.8078 (m-80) REVERT: L 124 GLN cc_start: 0.7850 (tt0) cc_final: 0.7110 (tt0) REVERT: L 165 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8708 (tp30) REVERT: L 211 ARG cc_start: 0.7818 (ptm-80) cc_final: 0.7241 (ttm110) REVERT: M 24 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8052 (ttp80) REVERT: M 79 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7267 (mt-10) REVERT: M 82 ASP cc_start: 0.8729 (m-30) cc_final: 0.8425 (m-30) REVERT: M 118 PHE cc_start: 0.8558 (m-80) cc_final: 0.8023 (m-80) REVERT: M 124 GLN cc_start: 0.7579 (tt0) cc_final: 0.6886 (tt0) REVERT: M 126 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7746 (tppt) REVERT: M 148 TRP cc_start: 0.6679 (m100) cc_final: 0.6477 (m100) REVERT: M 167 ASP cc_start: 0.7705 (t70) cc_final: 0.7489 (t70) outliers start: 35 outliers final: 28 residues processed: 230 average time/residue: 0.0786 time to fit residues: 26.3070 Evaluate side-chains 230 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 138 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 D residue 198 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 128 SER 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 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain L residue 29 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: 2.9990 chunk 110 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.156006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104834 restraints weight = 16223.292| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.53 r_work: 0.3100 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9593 Z= 0.236 Angle : 0.664 10.261 13080 Z= 0.335 Chirality : 0.044 0.145 1490 Planarity : 0.005 0.046 1608 Dihedral : 7.244 54.696 1710 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.52 % Allowed : 17.38 % 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: 1.62 (0.24), residues: 1192 helix: 1.66 (0.33), residues: 242 sheet: 2.04 (0.25), residues: 376 loop : 0.20 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 94 TYR 0.042 0.002 TYR C 94 PHE 0.015 0.002 PHE I 122 TRP 0.020 0.002 TRP D 89 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 9582) covalent geometry : angle 0.66046 (13058) SS BOND : bond 0.00576 ( 11) SS BOND : angle 1.81227 ( 22) hydrogen bonds : bond 0.04545 ( 434) hydrogen bonds : angle 4.93683 ( 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 235 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.7397 (p90) REVERT: C 175 LYS cc_start: 0.8881 (mmtp) cc_final: 0.8664 (mmtm) REVERT: C 204 GLN cc_start: 0.9194 (tp40) cc_final: 0.8970 (tt0) REVERT: D 116 LYS cc_start: 0.8501 (mttt) cc_final: 0.8034 (mttt) REVERT: H 5 GLN cc_start: 0.8598 (tt0) cc_final: 0.8153 (tp40) REVERT: H 64 LYS cc_start: 0.9136 (tttt) cc_final: 0.8673 (ttpp) REVERT: H 72 ASP cc_start: 0.8236 (t0) cc_final: 0.7624 (t0) REVERT: H 77 THR cc_start: 0.8968 (m) cc_final: 0.8243 (p) REVERT: H 85 GLU cc_start: 0.9129 (tp30) cc_final: 0.8905 (tp30) REVERT: H 86 ASP cc_start: 0.8447 (m-30) cc_final: 0.7964 (m-30) REVERT: H 154 TRP cc_start: 0.8242 (m100) cc_final: 0.7887 (m100) REVERT: H 161 SER cc_start: 0.8111 (m) cc_final: 0.7775 (p) REVERT: I 64 LYS cc_start: 0.9066 (tttt) cc_final: 0.8643 (ttpp) REVERT: I 72 ASP cc_start: 0.8268 (t0) cc_final: 0.7659 (t0) REVERT: I 77 THR cc_start: 0.8983 (m) cc_final: 0.8255 (p) REVERT: I 85 GLU cc_start: 0.9058 (tp30) cc_final: 0.8856 (tp30) REVERT: I 97 TYR cc_start: 0.9100 (t80) cc_final: 0.8814 (t80) REVERT: I 154 TRP cc_start: 0.8370 (m100) cc_final: 0.7993 (m100) REVERT: I 161 SER cc_start: 0.8222 (m) cc_final: 0.7930 (p) REVERT: I 214 LYS cc_start: 0.8394 (mttt) cc_final: 0.7879 (tptt) REVERT: L 79 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7328 (mt-10) REVERT: L 82 ASP cc_start: 0.8876 (m-30) cc_final: 0.8417 (m-30) REVERT: L 118 PHE cc_start: 0.8592 (m-80) cc_final: 0.7922 (m-80) REVERT: L 124 GLN cc_start: 0.7714 (tt0) cc_final: 0.6976 (tt0) REVERT: L 165 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8660 (tp30) REVERT: M 24 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8011 (ttp80) REVERT: M 79 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7302 (mt-10) REVERT: M 82 ASP cc_start: 0.8856 (m-30) cc_final: 0.8407 (m-30) REVERT: M 118 PHE cc_start: 0.8486 (m-80) cc_final: 0.7836 (m-80) REVERT: M 124 GLN cc_start: 0.7372 (tt0) cc_final: 0.6893 (tt0) REVERT: M 126 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7675 (tppt) REVERT: M 167 ASP cc_start: 0.7818 (t70) cc_final: 0.7592 (t0) outliers start: 36 outliers final: 29 residues processed: 223 average time/residue: 0.0703 time to fit residues: 23.0674 Evaluate side-chains 223 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 142 LYS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 123 SER 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 142 VAL Chi-restraints excluded: chain H residue 152 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 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain L residue 29 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 52 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107749 restraints weight = 15836.887| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.56 r_work: 0.3186 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9593 Z= 0.126 Angle : 0.585 9.755 13080 Z= 0.289 Chirality : 0.042 0.144 1490 Planarity : 0.004 0.043 1608 Dihedral : 7.026 55.430 1710 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.03 % Allowed : 18.55 % Favored : 78.42 % 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: 1.54 (0.25), residues: 1192 helix: 1.63 (0.34), residues: 254 sheet: 1.90 (0.25), residues: 394 loop : 0.10 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 211 TYR 0.043 0.002 TYR C 94 PHE 0.044 0.001 PHE C 62 TRP 0.019 0.001 TRP D 89 HIS 0.003 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9582) covalent geometry : angle 0.58340 (13058) SS BOND : bond 0.00432 ( 11) SS BOND : angle 1.06037 ( 22) hydrogen bonds : bond 0.03706 ( 434) hydrogen bonds : angle 4.58385 ( 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 227 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.7354 (p90) REVERT: C 116 LYS cc_start: 0.8609 (mttt) cc_final: 0.8405 (mmmt) REVERT: D 116 LYS cc_start: 0.8383 (mttt) cc_final: 0.7864 (mttt) REVERT: H 5 GLN cc_start: 0.8607 (tt0) cc_final: 0.8214 (tp40) REVERT: H 64 LYS cc_start: 0.9008 (tttt) cc_final: 0.8552 (ttpp) REVERT: H 72 ASP cc_start: 0.8212 (t0) cc_final: 0.7623 (t0) REVERT: H 77 THR cc_start: 0.8979 (m) cc_final: 0.8393 (p) REVERT: H 85 GLU cc_start: 0.9085 (tp30) cc_final: 0.8866 (tp30) REVERT: H 86 ASP cc_start: 0.8389 (m-30) cc_final: 0.7951 (m-30) REVERT: H 161 SER cc_start: 0.8110 (m) cc_final: 0.7780 (p) REVERT: I 64 LYS cc_start: 0.8951 (tttt) cc_final: 0.8536 (ttpp) REVERT: I 72 ASP cc_start: 0.8254 (t0) cc_final: 0.7673 (t0) REVERT: I 77 THR cc_start: 0.8992 (m) cc_final: 0.8410 (p) REVERT: I 85 GLU cc_start: 0.9054 (tp30) cc_final: 0.8853 (tp30) REVERT: I 97 TYR cc_start: 0.8986 (t80) cc_final: 0.8536 (t80) REVERT: I 154 TRP cc_start: 0.8388 (m100) cc_final: 0.8069 (m100) REVERT: I 161 SER cc_start: 0.8230 (m) cc_final: 0.7924 (p) REVERT: I 214 LYS cc_start: 0.8427 (mttt) cc_final: 0.7900 (tptt) REVERT: L 24 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7864 (ttp80) REVERT: L 79 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7427 (mt-10) REVERT: L 82 ASP cc_start: 0.8784 (m-30) cc_final: 0.8458 (m-30) REVERT: L 118 PHE cc_start: 0.8585 (m-80) cc_final: 0.7932 (m-80) REVERT: L 124 GLN cc_start: 0.7819 (tt0) cc_final: 0.7093 (tt0) REVERT: M 24 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8069 (ttp80) REVERT: M 79 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7387 (mt-10) REVERT: M 82 ASP cc_start: 0.8796 (m-30) cc_final: 0.8404 (m-30) REVERT: M 118 PHE cc_start: 0.8536 (m-80) cc_final: 0.7948 (m-80) REVERT: M 124 GLN cc_start: 0.7369 (tt0) cc_final: 0.6762 (tt0) REVERT: M 126 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7668 (tppt) REVERT: M 167 ASP cc_start: 0.7780 (t70) cc_final: 0.7543 (t0) outliers start: 31 outliers final: 26 residues processed: 218 average time/residue: 0.0738 time to fit residues: 23.4261 Evaluate side-chains 219 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 119 MET 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 183 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 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 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain L residue 29 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 73 optimal weight: 0.0270 chunk 35 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.161061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111042 restraints weight = 16105.946| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.50 r_work: 0.3247 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9593 Z= 0.090 Angle : 0.555 12.112 13080 Z= 0.271 Chirality : 0.041 0.142 1490 Planarity : 0.004 0.044 1608 Dihedral : 6.703 56.491 1710 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.25 % Allowed : 19.63 % Favored : 78.12 % 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: 1.92 (0.25), residues: 1192 helix: 2.02 (0.34), residues: 250 sheet: 2.02 (0.25), residues: 394 loop : 0.41 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 24 TYR 0.040 0.001 TYR C 94 PHE 0.031 0.001 PHE C 62 TRP 0.019 0.001 TRP D 89 HIS 0.002 0.000 HIS M 198 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 9582) covalent geometry : angle 0.55380 (13058) SS BOND : bond 0.00372 ( 11) SS BOND : angle 0.93524 ( 22) hydrogen bonds : bond 0.02926 ( 434) hydrogen bonds : angle 4.23682 ( 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 239 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8248 (OUTLIER) cc_final: 0.7172 (p90) REVERT: C 116 LYS cc_start: 0.8525 (mttt) cc_final: 0.8197 (mmmt) REVERT: C 175 LYS cc_start: 0.8775 (mmtp) cc_final: 0.8543 (mmtm) REVERT: C 197 MET cc_start: 0.9592 (ttm) cc_final: 0.9125 (tpp) REVERT: D 89 TRP cc_start: 0.8512 (OUTLIER) cc_final: 0.7290 (p90) REVERT: D 116 LYS cc_start: 0.8331 (mttt) cc_final: 0.7823 (mttt) REVERT: D 204 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8659 (tm-30) REVERT: H 5 GLN cc_start: 0.8610 (tt0) cc_final: 0.8249 (tp40) REVERT: H 64 LYS cc_start: 0.8794 (tttt) cc_final: 0.8366 (ttpp) REVERT: H 77 THR cc_start: 0.8940 (m) cc_final: 0.8487 (p) REVERT: H 85 GLU cc_start: 0.9055 (tp30) cc_final: 0.8823 (tp30) REVERT: H 86 ASP cc_start: 0.8371 (m-30) cc_final: 0.7925 (m-30) REVERT: H 161 SER cc_start: 0.8029 (m) cc_final: 0.7766 (p) REVERT: H 195 ILE cc_start: 0.6451 (mm) cc_final: 0.5955 (mp) REVERT: I 64 LYS cc_start: 0.8757 (tttt) cc_final: 0.8362 (ttpp) REVERT: I 72 ASP cc_start: 0.8123 (t0) cc_final: 0.7519 (t0) REVERT: I 77 THR cc_start: 0.8947 (m) cc_final: 0.8486 (p) REVERT: I 85 GLU cc_start: 0.9033 (tp30) cc_final: 0.8826 (tp30) REVERT: I 97 TYR cc_start: 0.8801 (t80) cc_final: 0.8487 (t80) REVERT: I 161 SER cc_start: 0.8184 (m) cc_final: 0.7880 (p) REVERT: I 214 LYS cc_start: 0.8477 (mttt) cc_final: 0.7980 (tptt) REVERT: L 79 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7292 (mt-10) REVERT: L 82 ASP cc_start: 0.8772 (m-30) cc_final: 0.8437 (m-30) REVERT: L 118 PHE cc_start: 0.8528 (m-80) cc_final: 0.7933 (m-80) REVERT: L 124 GLN cc_start: 0.7779 (tt0) cc_final: 0.7134 (tt0) REVERT: L 211 ARG cc_start: 0.7977 (ptm-80) cc_final: 0.7468 (ttm110) REVERT: M 24 ARG cc_start: 0.8390 (ttm110) cc_final: 0.8064 (ttp80) REVERT: M 79 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7328 (mt-10) REVERT: M 82 ASP cc_start: 0.8742 (m-30) cc_final: 0.8416 (m-30) REVERT: M 118 PHE cc_start: 0.8557 (m-80) cc_final: 0.8057 (m-80) REVERT: M 124 GLN cc_start: 0.7466 (tt0) cc_final: 0.6790 (tt0) REVERT: M 126 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7733 (tppt) REVERT: M 148 TRP cc_start: 0.6572 (m100) cc_final: 0.6358 (m100) REVERT: M 167 ASP cc_start: 0.7605 (t70) cc_final: 0.7328 (t0) outliers start: 23 outliers final: 18 residues processed: 229 average time/residue: 0.0701 time to fit residues: 23.6933 Evaluate side-chains 213 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 142 LYS Chi-restraints excluded: chain C residue 149 MET 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 152 VAL 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 I residue 197 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 39 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.156359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106574 restraints weight = 16043.487| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.40 r_work: 0.3167 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9593 Z= 0.204 Angle : 0.661 12.592 13080 Z= 0.329 Chirality : 0.043 0.162 1490 Planarity : 0.005 0.047 1608 Dihedral : 6.981 54.277 1710 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.15 % Allowed : 19.73 % Favored : 78.12 % 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: 1.59 (0.25), residues: 1192 helix: 1.84 (0.34), residues: 242 sheet: 1.94 (0.26), residues: 382 loop : 0.13 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 94 TYR 0.045 0.002 TYR C 94 PHE 0.039 0.002 PHE C 62 TRP 0.046 0.002 TRP I 154 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9582) covalent geometry : angle 0.65617 (13058) SS BOND : bond 0.00532 ( 11) SS BOND : angle 2.02438 ( 22) hydrogen bonds : bond 0.04170 ( 434) hydrogen bonds : angle 4.72688 ( 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 218 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8513 (OUTLIER) cc_final: 0.7361 (p90) REVERT: C 116 LYS cc_start: 0.8665 (mttt) cc_final: 0.8462 (mmmt) REVERT: D 116 LYS cc_start: 0.8481 (mttt) cc_final: 0.8031 (mttt) REVERT: H 5 GLN cc_start: 0.8589 (tt0) cc_final: 0.8154 (tp40) REVERT: H 64 LYS cc_start: 0.9093 (tttt) cc_final: 0.8633 (ttpp) REVERT: H 72 ASP cc_start: 0.8215 (t0) cc_final: 0.7610 (t0) REVERT: H 77 THR cc_start: 0.8988 (m) cc_final: 0.8370 (p) REVERT: H 85 GLU cc_start: 0.9098 (tp30) cc_final: 0.8873 (tp30) REVERT: H 86 ASP cc_start: 0.8408 (m-30) cc_final: 0.7942 (m-30) REVERT: H 154 TRP cc_start: 0.8272 (m100) cc_final: 0.7939 (m100) REVERT: H 161 SER cc_start: 0.8236 (m) cc_final: 0.7916 (p) REVERT: I 64 LYS cc_start: 0.9040 (tttt) cc_final: 0.8613 (ttpp) REVERT: I 72 ASP cc_start: 0.8230 (t0) cc_final: 0.7618 (t0) REVERT: I 77 THR cc_start: 0.9004 (m) cc_final: 0.8383 (p) REVERT: I 97 TYR cc_start: 0.9077 (t80) cc_final: 0.8747 (t80) REVERT: I 161 SER cc_start: 0.8334 (m) cc_final: 0.8104 (p) REVERT: I 214 LYS cc_start: 0.8453 (mttt) cc_final: 0.7859 (tptt) REVERT: L 79 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7453 (mt-10) REVERT: L 82 ASP cc_start: 0.8850 (m-30) cc_final: 0.8413 (m-30) REVERT: L 118 PHE cc_start: 0.8584 (m-80) cc_final: 0.7955 (m-80) REVERT: L 124 GLN cc_start: 0.7839 (tt0) cc_final: 0.7118 (tt0) REVERT: M 24 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8052 (ttp80) REVERT: M 79 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7285 (mt-10) REVERT: M 82 ASP cc_start: 0.8817 (m-30) cc_final: 0.8404 (m-30) REVERT: M 118 PHE cc_start: 0.8542 (m-80) cc_final: 0.7986 (m-80) REVERT: M 124 GLN cc_start: 0.7297 (tt0) cc_final: 0.6751 (tt0) REVERT: M 126 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7664 (tppt) REVERT: M 167 ASP cc_start: 0.7585 (t70) cc_final: 0.7344 (t0) outliers start: 22 outliers final: 20 residues processed: 211 average time/residue: 0.0778 time to fit residues: 24.0689 Evaluate side-chains 215 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 142 LYS 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 145 HIS Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain H residue 152 VAL 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 I residue 197 ASN Chi-restraints excluded: chain L residue 29 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.0020 chunk 109 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.161277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111628 restraints weight = 15729.987| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.57 r_work: 0.3238 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9593 Z= 0.096 Angle : 0.578 11.210 13080 Z= 0.280 Chirality : 0.041 0.154 1490 Planarity : 0.004 0.042 1608 Dihedral : 6.686 57.234 1710 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.95 % Allowed : 20.41 % Favored : 77.64 % 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: 1.68 (0.25), residues: 1192 helix: 1.74 (0.34), residues: 254 sheet: 2.07 (0.25), residues: 392 loop : 0.13 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 109 TYR 0.042 0.001 TYR C 94 PHE 0.027 0.001 PHE C 62 TRP 0.037 0.002 TRP I 154 HIS 0.002 0.000 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9582) covalent geometry : angle 0.57664 (13058) SS BOND : bond 0.00355 ( 11) SS BOND : angle 1.18301 ( 22) hydrogen bonds : bond 0.03052 ( 434) hydrogen bonds : angle 4.28993 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.17 seconds wall clock time: 40 minutes 53.04 seconds (2453.04 seconds total)