Starting phenix.real_space_refine on Sun Jul 27 17:52:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vja_21212/07_2025/6vja_21212.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vja_21212/07_2025/6vja_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vja_21212/07_2025/6vja_21212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vja_21212/07_2025/6vja_21212.map" model { file = "/net/cci-nas-00/data/ceres_data/6vja_21212/07_2025/6vja_21212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vja_21212/07_2025/6vja_21212.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.49, per 1000 atoms: 0.69 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.25 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: 2.74 Time building geometry restraints manager: 2.86 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: 0.02 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: 2.640 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.950 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (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 TRP 0.052 0.005 TRP M 91 HIS 0.011 0.003 HIS D 145 PHE 0.040 0.004 PHE H 100D TYR 0.038 0.007 TYR I 100C ARG 0.060 0.007 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.21402 ( 434) hydrogen bonds : angle 8.48481 ( 1206) SS BOND : bond 0.01058 ( 11) SS BOND : angle 2.51481 ( 22) covalent geometry : bond 0.01370 ( 9582) covalent geometry : angle 1.27006 (13058) *********************** 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 : 0.949 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 56 GLN cc_start: 0.8829 (mt0) cc_final: 0.8580 (mt0) 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: 0.7359 (mp) 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: 0.7737 (t0) REVERT: H 77 THR cc_start: 0.9088 (m) cc_final: 0.8497 (p) REVERT: H 86 ASP cc_start: 0.8579 (m-30) cc_final: 0.8012 (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: 0.7758 (tt0) REVERT: L 126 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7628 (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: 0.7451 (m-80) REVERT: M 124 GLN cc_start: 0.7880 (tt0) cc_final: 0.7628 (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: 0.3738 (t) outliers start: 5 outliers final: 1 residues processed: 306 average time/residue: 0.2069 time to fit residues: 88.7175 Evaluate side-chains 226 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.158236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109107 restraints weight = 15961.405| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.49 r_work: 0.3204 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9593 Z= 0.143 Angle : 0.662 9.130 13080 Z= 0.337 Chirality : 0.044 0.200 1490 Planarity : 0.004 0.044 1608 Dihedral : 7.707 59.805 1710 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.05 % Allowed : 10.64 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1192 helix: 1.01 (0.33), residues: 248 sheet: 2.14 (0.25), residues: 404 loop : 0.36 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 89 HIS 0.004 0.001 HIS D 145 PHE 0.014 0.001 PHE I 122 TYR 0.024 0.002 TYR D 94 ARG 0.003 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 434) hydrogen bonds : angle 5.47536 ( 1206) SS BOND : bond 0.00941 ( 11) SS BOND : angle 1.62519 ( 22) covalent geometry : bond 0.00315 ( 9582) covalent geometry : angle 0.65945 (13058) *********************** 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 280 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 TYR cc_start: 0.7227 (m-10) cc_final: 0.6945 (m-10) REVERT: C 116 LYS cc_start: 0.8558 (mttt) cc_final: 0.8274 (mmmt) REVERT: C 139 LEU cc_start: 0.8985 (mm) cc_final: 0.8702 (mm) REVERT: C 148 LYS cc_start: 0.6818 (pttp) cc_final: 0.6554 (ptmt) REVERT: C 175 LYS cc_start: 0.8595 (mmtp) cc_final: 0.8373 (mmtp) REVERT: D 62 PHE cc_start: 0.8724 (t80) cc_final: 0.8429 (t80) REVERT: D 89 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.7561 (p90) REVERT: D 116 LYS cc_start: 0.8285 (mttt) cc_final: 0.7739 (mttt) REVERT: D 175 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8398 (mmtp) REVERT: H 5 GLN cc_start: 0.8634 (tt0) cc_final: 0.8192 (tp40) REVERT: H 64 LYS cc_start: 0.8804 (tttt) cc_final: 0.8404 (ttpp) REVERT: H 72 ASP cc_start: 0.8167 (t0) cc_final: 0.7678 (t0) REVERT: H 77 THR cc_start: 0.8938 (m) cc_final: 0.8333 (p) REVERT: H 86 ASP cc_start: 0.8439 (m-30) cc_final: 0.8032 (m-30) REVERT: H 154 TRP cc_start: 0.8093 (m100) cc_final: 0.7675 (m100) REVERT: H 195 ILE cc_start: 0.7853 (mt) cc_final: 0.7549 (tt) REVERT: I 5 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: I 64 LYS cc_start: 0.8859 (tttt) cc_final: 0.8449 (ttpp) REVERT: I 72 ASP cc_start: 0.8274 (t0) cc_final: 0.7853 (t0) REVERT: I 77 THR cc_start: 0.8979 (m) cc_final: 0.8378 (p) REVERT: I 86 ASP cc_start: 0.8336 (m-30) cc_final: 0.7920 (m-30) REVERT: I 122 PHE cc_start: 0.7251 (m-10) cc_final: 0.7004 (m-10) REVERT: I 154 TRP cc_start: 0.8116 (m100) cc_final: 0.7708 (m100) REVERT: I 161 SER cc_start: 0.8147 (m) cc_final: 0.7747 (p) REVERT: I 214 LYS cc_start: 0.8462 (mttt) cc_final: 0.7966 (tptt) REVERT: L 24 ARG cc_start: 0.8128 (ttp-110) cc_final: 0.7912 (ttp80) REVERT: L 79 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7176 (mt-10) REVERT: L 82 ASP cc_start: 0.8803 (m-30) cc_final: 0.8466 (m-30) REVERT: L 118 PHE cc_start: 0.8637 (m-80) cc_final: 0.7759 (m-80) REVERT: L 124 GLN cc_start: 0.7945 (tt0) cc_final: 0.7375 (tt0) REVERT: M 24 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8131 (ttp80) REVERT: M 79 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7190 (mt-10) REVERT: M 82 ASP cc_start: 0.8820 (m-30) cc_final: 0.8492 (m-30) REVERT: M 118 PHE cc_start: 0.8558 (m-80) cc_final: 0.7758 (m-80) REVERT: M 124 GLN cc_start: 0.7838 (tt0) cc_final: 0.7439 (tt0) outliers start: 21 outliers final: 12 residues processed: 272 average time/residue: 0.2532 time to fit residues: 96.3432 Evaluate side-chains 237 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 134 SER 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 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 34 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.154295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103833 restraints weight = 16215.126| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.39 r_work: 0.3107 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 9593 Z= 0.297 Angle : 0.750 9.543 13080 Z= 0.387 Chirality : 0.047 0.263 1490 Planarity : 0.005 0.048 1608 Dihedral : 7.772 52.997 1710 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.88 % Allowed : 12.30 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1192 helix: 0.83 (0.33), residues: 246 sheet: 2.01 (0.26), residues: 370 loop : 0.10 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 89 HIS 0.004 0.001 HIS C 145 PHE 0.020 0.002 PHE H 100D TYR 0.040 0.003 TYR C 94 ARG 0.003 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05428 ( 434) hydrogen bonds : angle 5.54607 ( 1206) SS BOND : bond 0.00771 ( 11) SS BOND : angle 2.99095 ( 22) covalent geometry : bond 0.00708 ( 9582) covalent geometry : angle 0.74087 (13058) *********************** 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 266 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8626 (mttt) cc_final: 0.8183 (mttt) REVERT: C 139 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8718 (mm) REVERT: C 205 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8771 (tm-30) REVERT: D 62 PHE cc_start: 0.8699 (t80) cc_final: 0.8364 (t80) REVERT: D 116 LYS cc_start: 0.8502 (mttt) cc_final: 0.7970 (mttt) REVERT: D 137 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: H 5 GLN cc_start: 0.8578 (tt0) cc_final: 0.8130 (tp40) REVERT: H 64 LYS cc_start: 0.9135 (tttt) cc_final: 0.8695 (ttpp) REVERT: H 72 ASP cc_start: 0.8302 (t0) cc_final: 0.7824 (t0) REVERT: H 77 THR cc_start: 0.8990 (m) cc_final: 0.8251 (p) REVERT: H 85 GLU cc_start: 0.9150 (tp30) cc_final: 0.8937 (tp30) REVERT: H 86 ASP cc_start: 0.8404 (m-30) cc_final: 0.8024 (m-30) REVERT: H 154 TRP cc_start: 0.8264 (m100) cc_final: 0.7722 (m100) REVERT: H 161 SER cc_start: 0.8140 (m) cc_final: 0.7772 (p) REVERT: H 207 VAL cc_start: 0.8063 (t) cc_final: 0.7766 (p) REVERT: I 64 LYS cc_start: 0.9145 (tttt) cc_final: 0.8704 (ttpp) REVERT: I 72 ASP cc_start: 0.8308 (t0) cc_final: 0.7825 (t0) REVERT: I 77 THR cc_start: 0.9017 (m) cc_final: 0.8285 (p) REVERT: I 86 ASP cc_start: 0.8389 (m-30) cc_final: 0.7985 (m-30) REVERT: I 97 TYR cc_start: 0.9146 (t80) cc_final: 0.8919 (t80) REVERT: I 154 TRP cc_start: 0.8281 (m100) cc_final: 0.7748 (m100) REVERT: I 161 SER cc_start: 0.8249 (m) cc_final: 0.7958 (p) REVERT: I 214 LYS cc_start: 0.8411 (mttt) cc_final: 0.7911 (tptt) REVERT: L 79 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7283 (mt-10) REVERT: L 82 ASP cc_start: 0.8786 (m-30) cc_final: 0.8337 (m-30) REVERT: L 118 PHE cc_start: 0.8522 (m-80) cc_final: 0.7641 (m-80) REVERT: L 124 GLN cc_start: 0.7782 (tt0) cc_final: 0.7148 (tt0) REVERT: M 24 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8081 (ttp80) REVERT: M 79 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7360 (mt-10) REVERT: M 82 ASP cc_start: 0.8800 (m-30) cc_final: 0.8361 (m-30) REVERT: M 118 PHE cc_start: 0.8387 (m-80) cc_final: 0.7437 (m-80) REVERT: M 124 GLN cc_start: 0.7590 (tt0) cc_final: 0.7034 (tt0) REVERT: M 161 GLU cc_start: 0.8232 (pt0) cc_final: 0.7980 (pp20) outliers start: 50 outliers final: 35 residues processed: 245 average time/residue: 0.1861 time to fit residues: 65.7085 Evaluate side-chains 240 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 134 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 208 ILE 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 137 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 196 VAL 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 195 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 3 optimal weight: 0.5980 chunk 68 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107486 restraints weight = 15794.981| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.55 r_work: 0.3169 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9593 Z= 0.166 Angle : 0.629 7.955 13080 Z= 0.318 Chirality : 0.043 0.190 1490 Planarity : 0.005 0.044 1608 Dihedral : 7.398 56.546 1710 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.10 % Allowed : 14.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1192 helix: 1.22 (0.33), residues: 246 sheet: 1.91 (0.26), residues: 384 loop : 0.05 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 89 HIS 0.003 0.001 HIS C 145 PHE 0.013 0.002 PHE D 62 TYR 0.044 0.002 TYR C 94 ARG 0.002 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 434) hydrogen bonds : angle 4.97531 ( 1206) SS BOND : bond 0.00555 ( 11) SS BOND : angle 2.23100 ( 22) covalent geometry : bond 0.00390 ( 9582) covalent geometry : angle 0.62330 (13058) *********************** 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 255 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 94 TYR cc_start: 0.9427 (m-80) cc_final: 0.9176 (m-80) REVERT: C 116 LYS cc_start: 0.8634 (mttt) cc_final: 0.8281 (mmmt) REVERT: C 175 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8555 (mmtp) REVERT: D 116 LYS cc_start: 0.8426 (mttt) cc_final: 0.7851 (mttt) REVERT: D 139 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8764 (mm) REVERT: D 175 LYS cc_start: 0.8775 (mmtp) cc_final: 0.8518 (mmtp) REVERT: H 5 GLN cc_start: 0.8618 (tt0) cc_final: 0.8220 (tp40) REVERT: H 64 LYS cc_start: 0.9003 (tttt) cc_final: 0.8604 (ttpp) REVERT: H 72 ASP cc_start: 0.8322 (t0) cc_final: 0.7849 (t0) REVERT: H 77 THR cc_start: 0.9012 (m) cc_final: 0.8460 (p) REVERT: H 86 ASP cc_start: 0.8445 (m-30) cc_final: 0.8105 (m-30) REVERT: H 154 TRP cc_start: 0.8445 (m100) cc_final: 0.7990 (m100) REVERT: H 161 SER cc_start: 0.8156 (m) cc_final: 0.7806 (p) REVERT: H 207 VAL cc_start: 0.8092 (t) cc_final: 0.7882 (p) REVERT: I 64 LYS cc_start: 0.9039 (tttt) cc_final: 0.8600 (ttpp) REVERT: I 72 ASP cc_start: 0.8410 (t0) cc_final: 0.7947 (t0) REVERT: I 77 THR cc_start: 0.9029 (m) cc_final: 0.8452 (p) REVERT: I 86 ASP cc_start: 0.8305 (m-30) cc_final: 0.7931 (m-30) REVERT: I 97 TYR cc_start: 0.9081 (t80) cc_final: 0.8723 (t80) REVERT: I 154 TRP cc_start: 0.8411 (m100) cc_final: 0.7942 (m100) REVERT: I 161 SER cc_start: 0.8239 (m) cc_final: 0.7881 (p) REVERT: I 214 LYS cc_start: 0.8420 (mttt) cc_final: 0.7929 (tptt) REVERT: L 79 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7370 (mt-10) REVERT: L 82 ASP cc_start: 0.8766 (m-30) cc_final: 0.8411 (m-30) REVERT: L 118 PHE cc_start: 0.8597 (m-80) cc_final: 0.7822 (m-80) REVERT: L 124 GLN cc_start: 0.7866 (tt0) cc_final: 0.7223 (tt0) REVERT: M 24 ARG cc_start: 0.8524 (ttm110) cc_final: 0.8215 (ttp80) REVERT: M 79 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7357 (mt-10) REVERT: M 82 ASP cc_start: 0.8753 (m-30) cc_final: 0.8427 (m-30) REVERT: M 118 PHE cc_start: 0.8322 (m-80) cc_final: 0.7504 (m-80) REVERT: M 124 GLN cc_start: 0.7591 (tt0) cc_final: 0.7050 (tt0) REVERT: M 126 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7724 (tppt) REVERT: M 161 GLU cc_start: 0.8239 (pt0) cc_final: 0.7997 (pp20) outliers start: 42 outliers final: 28 residues processed: 242 average time/residue: 0.2624 time to fit residues: 91.7062 Evaluate side-chains 230 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 195 ILE 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 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN M 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.155686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105747 restraints weight = 15889.215| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.45 r_work: 0.3161 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9593 Z= 0.181 Angle : 0.626 9.820 13080 Z= 0.316 Chirality : 0.043 0.167 1490 Planarity : 0.005 0.047 1608 Dihedral : 7.358 59.058 1710 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.61 % Allowed : 16.02 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1192 helix: 1.37 (0.33), residues: 246 sheet: 1.86 (0.26), residues: 382 loop : -0.11 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 89 HIS 0.003 0.001 HIS C 145 PHE 0.019 0.001 PHE D 62 TYR 0.038 0.002 TYR C 94 ARG 0.002 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 434) hydrogen bonds : angle 4.91134 ( 1206) SS BOND : bond 0.00521 ( 11) SS BOND : angle 1.57663 ( 22) covalent geometry : bond 0.00427 ( 9582) covalent geometry : angle 0.62357 (13058) *********************** 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 237 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8734 (OUTLIER) cc_final: 0.7397 (p90) REVERT: C 197 MET cc_start: 0.9562 (ttm) cc_final: 0.9097 (tpp) REVERT: D 116 LYS cc_start: 0.8442 (mttt) cc_final: 0.7912 (mttt) REVERT: H 5 GLN cc_start: 0.8558 (tt0) cc_final: 0.8133 (tp40) REVERT: H 64 LYS cc_start: 0.9055 (tttt) cc_final: 0.8616 (ttpp) REVERT: H 72 ASP cc_start: 0.8226 (t0) cc_final: 0.7700 (t0) REVERT: H 77 THR cc_start: 0.8972 (m) cc_final: 0.8350 (p) REVERT: H 86 ASP cc_start: 0.8341 (m-30) cc_final: 0.7960 (m-30) REVERT: H 154 TRP cc_start: 0.8376 (m100) cc_final: 0.7920 (m100) REVERT: H 161 SER cc_start: 0.8064 (m) cc_final: 0.7730 (p) REVERT: H 207 VAL cc_start: 0.8003 (t) cc_final: 0.7791 (p) REVERT: I 64 LYS cc_start: 0.9029 (tttt) cc_final: 0.8573 (ttpp) REVERT: I 72 ASP cc_start: 0.8234 (t0) cc_final: 0.7701 (t0) REVERT: I 77 THR cc_start: 0.9012 (m) cc_final: 0.8347 (p) REVERT: I 86 ASP cc_start: 0.8283 (m-30) cc_final: 0.7851 (m-30) REVERT: I 97 TYR cc_start: 0.9035 (t80) cc_final: 0.8660 (t80) REVERT: I 154 TRP cc_start: 0.8378 (m100) cc_final: 0.7932 (m100) REVERT: I 161 SER cc_start: 0.8127 (m) cc_final: 0.7782 (p) REVERT: I 214 LYS cc_start: 0.8372 (mttt) cc_final: 0.7826 (tptt) REVERT: L 79 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7309 (mt-10) REVERT: L 82 ASP cc_start: 0.8839 (m-30) cc_final: 0.8411 (m-30) REVERT: L 118 PHE cc_start: 0.8538 (m-80) cc_final: 0.7767 (m-80) REVERT: L 124 GLN cc_start: 0.7820 (tt0) cc_final: 0.7147 (tt0) REVERT: M 24 ARG cc_start: 0.8429 (ttm110) cc_final: 0.8085 (ttp80) REVERT: M 79 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7298 (mt-10) REVERT: M 82 ASP cc_start: 0.8844 (m-30) cc_final: 0.8421 (m-30) REVERT: M 118 PHE cc_start: 0.8347 (m-80) cc_final: 0.7645 (m-80) REVERT: M 124 GLN cc_start: 0.7542 (tt0) cc_final: 0.7018 (tt0) REVERT: M 126 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7624 (tppt) REVERT: M 158 ASN cc_start: 0.7638 (t160) cc_final: 0.6570 (p0) REVERT: M 161 GLU cc_start: 0.8288 (pt0) cc_final: 0.8008 (pp20) outliers start: 37 outliers final: 29 residues processed: 225 average time/residue: 0.2084 time to fit residues: 65.9989 Evaluate side-chains 226 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 195 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.157293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106773 restraints weight = 15894.205| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.45 r_work: 0.3165 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9593 Z= 0.177 Angle : 0.616 10.229 13080 Z= 0.311 Chirality : 0.043 0.155 1490 Planarity : 0.005 0.044 1608 Dihedral : 7.328 57.034 1710 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.81 % Allowed : 16.60 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1192 helix: 1.60 (0.33), residues: 238 sheet: 1.79 (0.25), residues: 392 loop : -0.09 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 89 HIS 0.002 0.001 HIS M 34 PHE 0.022 0.002 PHE D 62 TYR 0.044 0.002 TYR C 94 ARG 0.002 0.000 ARG L 211 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 434) hydrogen bonds : angle 4.85722 ( 1206) SS BOND : bond 0.00510 ( 11) SS BOND : angle 1.35902 ( 22) covalent geometry : bond 0.00415 ( 9582) covalent geometry : angle 0.61364 (13058) *********************** 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 240 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8685 (OUTLIER) cc_final: 0.7093 (p90) REVERT: C 116 LYS cc_start: 0.8655 (mttt) cc_final: 0.8397 (mmmt) REVERT: D 116 LYS cc_start: 0.8420 (mttt) cc_final: 0.7907 (mttt) REVERT: H 5 GLN cc_start: 0.8570 (tt0) cc_final: 0.8142 (tp40) REVERT: H 64 LYS cc_start: 0.9056 (tttt) cc_final: 0.8603 (ttpp) REVERT: H 72 ASP cc_start: 0.8206 (t0) cc_final: 0.7668 (t0) REVERT: H 77 THR cc_start: 0.8979 (m) cc_final: 0.8333 (p) REVERT: H 86 ASP cc_start: 0.8315 (m-30) cc_final: 0.7909 (m-30) REVERT: H 154 TRP cc_start: 0.8391 (m100) cc_final: 0.7875 (m100) REVERT: H 161 SER cc_start: 0.8119 (m) cc_final: 0.7778 (p) REVERT: H 207 VAL cc_start: 0.7973 (t) cc_final: 0.7753 (p) REVERT: I 64 LYS cc_start: 0.9049 (tttt) cc_final: 0.8585 (ttpp) REVERT: I 72 ASP cc_start: 0.8218 (t0) cc_final: 0.7665 (t0) REVERT: I 77 THR cc_start: 0.9009 (m) cc_final: 0.8348 (p) REVERT: I 86 ASP cc_start: 0.8257 (m-30) cc_final: 0.7815 (m-30) REVERT: I 97 TYR cc_start: 0.9029 (t80) cc_final: 0.8637 (t80) REVERT: I 154 TRP cc_start: 0.8401 (m100) cc_final: 0.7963 (m100) REVERT: I 161 SER cc_start: 0.8195 (m) cc_final: 0.7888 (p) REVERT: I 214 LYS cc_start: 0.8342 (mttt) cc_final: 0.7785 (tptt) REVERT: L 79 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7451 (mt-10) REVERT: L 82 ASP cc_start: 0.8839 (m-30) cc_final: 0.8424 (m-30) REVERT: L 118 PHE cc_start: 0.8536 (m-80) cc_final: 0.7722 (m-80) REVERT: L 124 GLN cc_start: 0.7758 (tt0) cc_final: 0.7121 (tt0) REVERT: M 24 ARG cc_start: 0.8409 (ttm110) cc_final: 0.8065 (ttp80) REVERT: M 79 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7391 (mt-10) REVERT: M 82 ASP cc_start: 0.8852 (m-30) cc_final: 0.8440 (m-30) REVERT: M 118 PHE cc_start: 0.8295 (m-80) cc_final: 0.7614 (m-80) REVERT: M 124 GLN cc_start: 0.7473 (tt0) cc_final: 0.7000 (tt0) REVERT: M 126 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7623 (tppt) REVERT: M 158 ASN cc_start: 0.7583 (t0) cc_final: 0.7362 (t0) outliers start: 39 outliers final: 28 residues processed: 230 average time/residue: 0.2001 time to fit residues: 65.5713 Evaluate side-chains 217 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 141 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain H residue 12 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 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.158567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107802 restraints weight = 16067.859| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.49 r_work: 0.3159 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9593 Z= 0.142 Angle : 0.592 10.659 13080 Z= 0.295 Chirality : 0.042 0.140 1490 Planarity : 0.005 0.045 1608 Dihedral : 7.194 54.925 1710 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.32 % Allowed : 17.97 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1192 helix: 1.70 (0.33), residues: 238 sheet: 1.82 (0.25), residues: 392 loop : -0.02 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.001 0.000 HIS M 34 PHE 0.015 0.001 PHE D 62 TYR 0.041 0.002 TYR C 94 ARG 0.002 0.000 ARG L 211 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 434) hydrogen bonds : angle 4.70902 ( 1206) SS BOND : bond 0.00496 ( 11) SS BOND : angle 1.16368 ( 22) covalent geometry : bond 0.00331 ( 9582) covalent geometry : angle 0.59011 (13058) *********************** 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 233 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.6936 (p90) REVERT: C 116 LYS cc_start: 0.8672 (mttt) cc_final: 0.8406 (mmmt) REVERT: C 197 MET cc_start: 0.9561 (ttm) cc_final: 0.9108 (tpp) REVERT: D 116 LYS cc_start: 0.8421 (mttt) cc_final: 0.7899 (mttt) REVERT: H 5 GLN cc_start: 0.8558 (tt0) cc_final: 0.8133 (tp40) REVERT: H 64 LYS cc_start: 0.8999 (tttt) cc_final: 0.8552 (ttpp) REVERT: H 72 ASP cc_start: 0.8154 (t0) cc_final: 0.7598 (t0) REVERT: H 77 THR cc_start: 0.8981 (m) cc_final: 0.8400 (p) REVERT: H 86 ASP cc_start: 0.8273 (m-30) cc_final: 0.7881 (m-30) REVERT: H 154 TRP cc_start: 0.8250 (m100) cc_final: 0.7807 (m100) REVERT: H 161 SER cc_start: 0.8055 (m) cc_final: 0.7718 (p) REVERT: H 207 VAL cc_start: 0.7920 (t) cc_final: 0.7683 (p) REVERT: I 64 LYS cc_start: 0.8997 (tttt) cc_final: 0.8535 (ttpp) REVERT: I 72 ASP cc_start: 0.8180 (t0) cc_final: 0.7615 (t0) REVERT: I 77 THR cc_start: 0.8998 (m) cc_final: 0.8398 (p) REVERT: I 86 ASP cc_start: 0.8215 (m-30) cc_final: 0.7805 (m-30) REVERT: I 97 TYR cc_start: 0.9009 (t80) cc_final: 0.8620 (t80) REVERT: I 154 TRP cc_start: 0.8397 (m100) cc_final: 0.7952 (m100) REVERT: I 161 SER cc_start: 0.8221 (m) cc_final: 0.7911 (p) REVERT: I 214 LYS cc_start: 0.8362 (mttt) cc_final: 0.7831 (tptt) REVERT: L 79 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7379 (mt-10) REVERT: L 82 ASP cc_start: 0.8809 (m-30) cc_final: 0.8460 (m-30) REVERT: L 118 PHE cc_start: 0.8572 (m-80) cc_final: 0.7807 (m-80) REVERT: L 124 GLN cc_start: 0.7778 (tt0) cc_final: 0.7132 (tt0) REVERT: M 24 ARG cc_start: 0.8362 (ttm110) cc_final: 0.7962 (ttp80) REVERT: M 79 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7476 (mt-10) REVERT: M 82 ASP cc_start: 0.8842 (m-30) cc_final: 0.8427 (m-30) REVERT: M 118 PHE cc_start: 0.8322 (m-80) cc_final: 0.7685 (m-80) REVERT: M 124 GLN cc_start: 0.7468 (tt0) cc_final: 0.6987 (tt0) REVERT: M 126 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7660 (tppt) REVERT: M 167 ASP cc_start: 0.7637 (t70) cc_final: 0.7388 (t0) outliers start: 34 outliers final: 24 residues processed: 222 average time/residue: 0.3234 time to fit residues: 103.9169 Evaluate side-chains 222 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain H residue 12 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 0.8980 chunk 98 optimal weight: 0.0040 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN M 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.160025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.110276 restraints weight = 16118.947| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.49 r_work: 0.3168 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4242 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= 0.105 Angle : 0.565 10.605 13080 Z= 0.281 Chirality : 0.041 0.159 1490 Planarity : 0.004 0.049 1608 Dihedral : 7.044 55.778 1710 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.12 % Allowed : 18.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1192 helix: 1.61 (0.33), residues: 250 sheet: 1.90 (0.25), residues: 388 loop : -0.00 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.001 0.000 HIS D 145 PHE 0.012 0.001 PHE D 62 TYR 0.016 0.001 TYR I 100C ARG 0.001 0.000 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 434) hydrogen bonds : angle 4.45716 ( 1206) SS BOND : bond 0.00398 ( 11) SS BOND : angle 0.82724 ( 22) covalent geometry : bond 0.00237 ( 9582) covalent geometry : angle 0.56491 (13058) *********************** 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 241 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8449 (OUTLIER) cc_final: 0.6834 (p90) REVERT: C 116 LYS cc_start: 0.8616 (mttt) cc_final: 0.8263 (mmmt) REVERT: C 197 MET cc_start: 0.9556 (ttm) cc_final: 0.9130 (tpp) REVERT: C 204 GLN cc_start: 0.8919 (tp40) cc_final: 0.8460 (tp40) REVERT: D 89 TRP cc_start: 0.8486 (OUTLIER) cc_final: 0.7199 (p90) REVERT: D 116 LYS cc_start: 0.8378 (mttt) cc_final: 0.7862 (mttt) REVERT: D 197 MET cc_start: 0.9490 (ttm) cc_final: 0.9082 (tpp) REVERT: H 5 GLN cc_start: 0.8555 (tt0) cc_final: 0.8129 (tp40) REVERT: H 64 LYS cc_start: 0.8863 (tttt) cc_final: 0.8420 (ttpp) REVERT: H 72 ASP cc_start: 0.8071 (t0) cc_final: 0.7484 (t0) REVERT: H 77 THR cc_start: 0.8941 (m) cc_final: 0.8436 (p) REVERT: H 161 SER cc_start: 0.8030 (m) cc_final: 0.7690 (p) REVERT: H 198 VAL cc_start: 0.8915 (t) cc_final: 0.8647 (m) REVERT: I 64 LYS cc_start: 0.8828 (tttt) cc_final: 0.8415 (ttpp) REVERT: I 72 ASP cc_start: 0.8102 (t0) cc_final: 0.7516 (t0) REVERT: I 77 THR cc_start: 0.8956 (m) cc_final: 0.8430 (p) REVERT: I 97 TYR cc_start: 0.8932 (t80) cc_final: 0.8391 (t80) REVERT: I 154 TRP cc_start: 0.8393 (m100) cc_final: 0.8083 (m100) REVERT: I 161 SER cc_start: 0.8177 (m) cc_final: 0.7874 (p) REVERT: I 214 LYS cc_start: 0.8380 (mttt) cc_final: 0.7840 (tptt) REVERT: L 24 ARG cc_start: 0.8093 (ttp-110) cc_final: 0.7793 (ttp80) REVERT: L 79 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7368 (mt-10) REVERT: L 82 ASP cc_start: 0.8813 (m-30) cc_final: 0.8468 (m-30) REVERT: L 118 PHE cc_start: 0.8545 (m-80) cc_final: 0.7851 (m-80) REVERT: L 124 GLN cc_start: 0.7765 (tt0) cc_final: 0.7106 (tt0) REVERT: L 211 ARG cc_start: 0.7220 (ptm-80) cc_final: 0.6921 (ptm-80) REVERT: M 24 ARG cc_start: 0.8368 (ttm110) cc_final: 0.8038 (ttp80) REVERT: M 79 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7361 (mt-10) REVERT: M 82 ASP cc_start: 0.8792 (m-30) cc_final: 0.8460 (m-30) REVERT: M 118 PHE cc_start: 0.8359 (m-80) cc_final: 0.7737 (m-80) REVERT: M 124 GLN cc_start: 0.7613 (tt0) cc_final: 0.7166 (tt0) REVERT: M 167 ASP cc_start: 0.7608 (t70) cc_final: 0.7258 (t70) outliers start: 32 outliers final: 21 residues processed: 229 average time/residue: 0.2430 time to fit residues: 80.4017 Evaluate side-chains 217 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain 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 145 HIS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 100 TYR 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 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 0.0170 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.158969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109206 restraints weight = 15826.649| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.47 r_work: 0.3221 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4378 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= 0.106 Angle : 0.588 10.661 13080 Z= 0.286 Chirality : 0.041 0.158 1490 Planarity : 0.005 0.045 1608 Dihedral : 6.897 55.757 1710 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.34 % Allowed : 19.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1192 helix: 1.55 (0.33), residues: 254 sheet: 1.94 (0.25), residues: 388 loop : 0.01 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.001 0.000 HIS D 63 PHE 0.023 0.001 PHE D 62 TYR 0.016 0.001 TYR I 100C ARG 0.002 0.000 ARG L 211 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 434) hydrogen bonds : angle 4.38820 ( 1206) SS BOND : bond 0.00344 ( 11) SS BOND : angle 0.81733 ( 22) covalent geometry : bond 0.00239 ( 9582) covalent geometry : angle 0.58710 (13058) *********************** 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 228 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8440 (OUTLIER) cc_final: 0.6896 (p90) REVERT: C 116 LYS cc_start: 0.8572 (mttt) cc_final: 0.8206 (mmmt) REVERT: C 197 MET cc_start: 0.9565 (ttm) cc_final: 0.9121 (tpp) REVERT: C 204 GLN cc_start: 0.8918 (tp40) cc_final: 0.8570 (tp40) REVERT: D 89 TRP cc_start: 0.8490 (OUTLIER) cc_final: 0.7143 (p90) REVERT: D 116 LYS cc_start: 0.8392 (mttt) cc_final: 0.7898 (mttt) REVERT: D 197 MET cc_start: 0.9465 (ttm) cc_final: 0.9064 (tpp) REVERT: H 5 GLN cc_start: 0.8545 (tt0) cc_final: 0.8130 (tp40) REVERT: H 64 LYS cc_start: 0.8827 (tttt) cc_final: 0.8379 (ttpp) REVERT: H 72 ASP cc_start: 0.8074 (t0) cc_final: 0.7487 (t0) REVERT: H 77 THR cc_start: 0.8944 (m) cc_final: 0.8464 (p) REVERT: H 161 SER cc_start: 0.8054 (m) cc_final: 0.7790 (p) REVERT: H 198 VAL cc_start: 0.8911 (t) cc_final: 0.8658 (m) REVERT: I 64 LYS cc_start: 0.8798 (tttt) cc_final: 0.8394 (ttpp) REVERT: I 72 ASP cc_start: 0.8088 (t0) cc_final: 0.7485 (t0) REVERT: I 77 THR cc_start: 0.8961 (m) cc_final: 0.8454 (p) REVERT: I 97 TYR cc_start: 0.8905 (t80) cc_final: 0.8379 (t80) REVERT: I 154 TRP cc_start: 0.8396 (m100) cc_final: 0.8104 (m100) REVERT: I 161 SER cc_start: 0.8233 (m) cc_final: 0.7940 (p) REVERT: I 214 LYS cc_start: 0.8427 (mttt) cc_final: 0.7894 (tptt) REVERT: L 79 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7332 (mt-10) REVERT: L 82 ASP cc_start: 0.8812 (m-30) cc_final: 0.8469 (m-30) REVERT: L 118 PHE cc_start: 0.8628 (m-80) cc_final: 0.8086 (m-80) REVERT: L 124 GLN cc_start: 0.7800 (tt0) cc_final: 0.7115 (tt0) REVERT: L 211 ARG cc_start: 0.7202 (ptm-80) cc_final: 0.6891 (ptm-80) REVERT: M 24 ARG cc_start: 0.8362 (ttm110) cc_final: 0.8031 (ttp80) REVERT: M 79 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7379 (mt-10) REVERT: M 82 ASP cc_start: 0.8762 (m-30) cc_final: 0.8443 (m-30) REVERT: M 118 PHE cc_start: 0.8359 (m-80) cc_final: 0.7786 (m-80) REVERT: M 124 GLN cc_start: 0.7501 (tt0) cc_final: 0.7005 (tt0) REVERT: M 167 ASP cc_start: 0.7435 (t70) cc_final: 0.7109 (t70) outliers start: 24 outliers final: 20 residues processed: 220 average time/residue: 0.1804 time to fit residues: 57.0698 Evaluate side-chains 214 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain D residue 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 149 MET Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 100 TYR 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 117 ILE Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.157802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107562 restraints weight = 16209.399| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.49 r_work: 0.3207 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4405 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= 0.122 Angle : 0.597 10.751 13080 Z= 0.291 Chirality : 0.041 0.156 1490 Planarity : 0.004 0.045 1608 Dihedral : 6.856 56.500 1710 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.54 % Allowed : 19.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1192 helix: 1.89 (0.34), residues: 242 sheet: 1.86 (0.25), residues: 390 loop : 0.08 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 89 HIS 0.001 0.000 HIS D 145 PHE 0.021 0.001 PHE D 62 TYR 0.018 0.001 TYR I 100C ARG 0.002 0.000 ARG L 211 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 434) hydrogen bonds : angle 4.44441 ( 1206) SS BOND : bond 0.00395 ( 11) SS BOND : angle 0.89970 ( 22) covalent geometry : bond 0.00283 ( 9582) covalent geometry : angle 0.59641 (13058) ********************** 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 222 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8487 (OUTLIER) cc_final: 0.7250 (p90) REVERT: C 116 LYS cc_start: 0.8548 (mttt) cc_final: 0.8230 (mmmt) REVERT: C 197 MET cc_start: 0.9575 (ttm) cc_final: 0.9115 (tpp) REVERT: C 204 GLN cc_start: 0.8924 (tp40) cc_final: 0.8571 (tp40) REVERT: D 89 TRP cc_start: 0.8419 (OUTLIER) cc_final: 0.7004 (p90) REVERT: D 116 LYS cc_start: 0.8451 (mttt) cc_final: 0.7979 (mttt) REVERT: D 197 MET cc_start: 0.9489 (ttm) cc_final: 0.9117 (tpp) REVERT: H 5 GLN cc_start: 0.8566 (tt0) cc_final: 0.8143 (tp40) REVERT: H 64 LYS cc_start: 0.8943 (tttt) cc_final: 0.8480 (ttpp) REVERT: H 72 ASP cc_start: 0.8112 (t0) cc_final: 0.7525 (t0) REVERT: H 77 THR cc_start: 0.8957 (m) cc_final: 0.8447 (p) REVERT: H 161 SER cc_start: 0.8174 (m) cc_final: 0.7860 (p) REVERT: H 198 VAL cc_start: 0.8911 (t) cc_final: 0.8661 (m) REVERT: I 64 LYS cc_start: 0.8895 (tttt) cc_final: 0.8484 (ttpp) REVERT: I 72 ASP cc_start: 0.8115 (t0) cc_final: 0.7514 (t0) REVERT: I 77 THR cc_start: 0.8975 (m) cc_final: 0.8457 (p) REVERT: I 97 TYR cc_start: 0.8967 (t80) cc_final: 0.8441 (t80) REVERT: I 154 TRP cc_start: 0.8394 (m100) cc_final: 0.8035 (m100) REVERT: I 161 SER cc_start: 0.8361 (m) cc_final: 0.8069 (p) REVERT: I 214 LYS cc_start: 0.8447 (mttt) cc_final: 0.7939 (tptt) REVERT: L 79 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7355 (mt-10) REVERT: L 82 ASP cc_start: 0.8804 (m-30) cc_final: 0.8460 (m-30) REVERT: L 118 PHE cc_start: 0.8547 (m-80) cc_final: 0.8047 (m-80) REVERT: L 124 GLN cc_start: 0.7739 (tt0) cc_final: 0.7056 (tt0) REVERT: L 148 TRP cc_start: 0.7119 (m100) cc_final: 0.6863 (m100) REVERT: L 211 ARG cc_start: 0.7189 (ptm-80) cc_final: 0.6863 (ptm-80) REVERT: M 24 ARG cc_start: 0.8367 (ttm110) cc_final: 0.8033 (ttp80) REVERT: M 79 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7406 (mt-10) REVERT: M 82 ASP cc_start: 0.8765 (m-30) cc_final: 0.8440 (m-30) REVERT: M 118 PHE cc_start: 0.8378 (m-80) cc_final: 0.7804 (m-80) REVERT: M 124 GLN cc_start: 0.7503 (tt0) cc_final: 0.6983 (tt0) REVERT: M 167 ASP cc_start: 0.7482 (t70) cc_final: 0.7156 (t70) outliers start: 26 outliers final: 23 residues processed: 213 average time/residue: 0.1784 time to fit residues: 54.8101 Evaluate side-chains 219 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 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 145 HIS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 100 TYR 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 117 ILE Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 71 optimal weight: 10.0000 chunk 54 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 77 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.162537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113251 restraints weight = 15877.057| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.59 r_work: 0.3265 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9593 Z= 0.092 Angle : 0.585 15.930 13080 Z= 0.279 Chirality : 0.041 0.170 1490 Planarity : 0.004 0.043 1608 Dihedral : 6.633 57.767 1710 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.25 % Allowed : 19.53 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1192 helix: 1.75 (0.34), residues: 250 sheet: 1.92 (0.25), residues: 392 loop : 0.23 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.003 0.001 HIS D 63 PHE 0.016 0.001 PHE D 62 TYR 0.033 0.001 TYR D 94 ARG 0.003 0.000 ARG L 211 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 434) hydrogen bonds : angle 4.18200 ( 1206) SS BOND : bond 0.00338 ( 11) SS BOND : angle 0.62608 ( 22) covalent geometry : bond 0.00195 ( 9582) covalent geometry : angle 0.58535 (13058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5474.07 seconds wall clock time: 99 minutes 49.77 seconds (5989.77 seconds total)