Starting phenix.real_space_refine on Fri Mar 14 04:44:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vja_21212/03_2025/6vja_21212.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vja_21212/03_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_21212/03_2025/6vja_21212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vja_21212/03_2025/6vja_21212.map" model { file = "/net/cci-nas-00/data/ceres_data/6vja_21212/03_2025/6vja_21212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vja_21212/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.15, per 1000 atoms: 0.66 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 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: 1.38 Creating SS restraints... Processing helix chain 'C' and resid 47 through 71 removed outlier: 4.541A pdb=" N THR C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 63 " --> pdb=" O ASN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 85 through 97 removed outlier: 3.867A pdb=" N TRP C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 114 through 143 removed outlier: 3.759A pdb=" N ILE C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 177 through 206 removed outlier: 3.770A pdb=" N GLN C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN C 204 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 71 removed outlier: 4.406A pdb=" N THR D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS D 63 " --> pdb=" O ASN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.606A pdb=" N TRP D 89 " --> pdb=" O TRP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 114 through 141 removed outlier: 3.559A pdb=" N ILE D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 124 " --> pdb=" O ASN D 120 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 177 through 206 removed outlier: 3.591A pdb=" N GLN D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.838A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 removed outlier: 4.458A pdb=" N GLY H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.707A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 129 No H-bonds generated for 'chain 'H' and resid 127 through 129' Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.797A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 4.410A pdb=" N GLY I 65 " --> pdb=" O GLN I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.706A pdb=" N SER I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'I' and resid 156 through 158 No H-bonds generated for 'chain 'I' and resid 156 through 158' Processing helix chain 'I' and resid 187 through 189 No H-bonds generated for 'chain 'I' and resid 187 through 189' Processing helix chain 'I' and resid 201 through 204 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.970A pdb=" N ALA L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.928A pdb=" N ALA M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.863A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.554A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN H 33 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.554A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG H 94 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.572A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 132 removed outlier: 6.011A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.020A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.882A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.552A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN I 33 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.552A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG I 94 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP I 100A" --> pdb=" O TYR I 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 120 through 124 removed outlier: 5.978A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 131 through 132 removed outlier: 5.978A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 151 through 154 removed outlier: 4.019A pdb=" N TYR I 194 " --> pdb=" O VAL I 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.544A pdb=" N TRP L 35 " --> pdb=" O TRP L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.582A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.790A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA L 130 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.518A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'M' and resid 10 through 13 removed outlier: 4.158A pdb=" N ALA M 13 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP M 35 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 10 through 13 removed outlier: 4.158A pdb=" N ALA M 13 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 114 through 118 removed outlier: 3.781A pdb=" N VAL M 133 " --> pdb=" O PHE M 118 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA M 130 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 153 through 154 removed outlier: 3.507A pdb=" N CYS M 194 " --> pdb=" O LYS M 207 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS M 207 " --> pdb=" O CYS M 194 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 2.82 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: 1.880 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.560 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- 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 9582 Z= 0.883 Angle : 1.270 10.980 13058 Z= 0.673 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 *********************** 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 : 1.075 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: 0.2018 time to fit residues: 85.8493 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 : 1.007 ------------------------------------------------------------------------------- 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: 3.9990 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 9582 Z= 0.201 Angle : 0.659 9.130 13058 Z= 0.336 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 *********************** 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 : 1.007 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: 0.1982 time to fit residues: 76.1689 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 : 0.933 ------------------------------------------------------------------------------- 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 9582 Z= 0.457 Angle : 0.741 8.962 13058 Z= 0.383 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 *********************** 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 : 0.985 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: 0.1814 time to fit residues: 63.8678 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 : 0.985 ------------------------------------------------------------------------------- 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: 6.9990 chunk 3 optimal weight: 0.5980 chunk 68 optimal weight: 20.0000 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: 10.0000 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.156711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105861 restraints weight = 15848.146| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.54 r_work: 0.3162 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9582 Z= 0.307 Angle : 0.651 7.753 13058 Z= 0.331 Chirality : 0.044 0.200 1490 Planarity : 0.005 0.044 1608 Dihedral : 7.501 56.493 1710 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.20 % Allowed : 14.16 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.28 (0.24), residues: 1192 helix: 1.09 (0.33), residues: 246 sheet: 2.02 (0.26), residues: 368 loop : -0.01 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 89 HIS 0.003 0.001 HIS M 34 PHE 0.015 0.002 PHE I 100D TYR 0.044 0.002 TYR C 94 ARG 0.002 0.000 ARG D 109 *********************** 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 254 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: C 94 TYR cc_start: 0.9437 (m-80) cc_final: 0.9192 (m-80) REVERT: C 116 LYS cc_start: 0.8640 (mttt) cc_final: 0.8304 (mmmt) REVERT: C 175 LYS cc_start: 0.8817 (mmtp) cc_final: 0.8585 (mmtp) REVERT: D 116 LYS cc_start: 0.8447 (mttt) cc_final: 0.7874 (mttt) REVERT: D 137 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: D 139 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8767 (mm) REVERT: D 175 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8531 (mmtp) REVERT: H 5 GLN cc_start: 0.8636 (tt0) cc_final: 0.8229 (tp40) REVERT: H 64 LYS cc_start: 0.9047 (tttt) cc_final: 0.8632 (ttpp) REVERT: H 72 ASP cc_start: 0.8353 (t0) cc_final: 0.7902 (t0) REVERT: H 77 THR cc_start: 0.9004 (m) cc_final: 0.8363 (p) REVERT: H 86 ASP cc_start: 0.8462 (m-30) cc_final: 0.8122 (m-30) REVERT: H 154 TRP cc_start: 0.8419 (m100) cc_final: 0.7957 (m100) REVERT: H 161 SER cc_start: 0.8164 (m) cc_final: 0.7814 (p) REVERT: H 207 VAL cc_start: 0.8068 (t) cc_final: 0.7859 (p) REVERT: I 64 LYS cc_start: 0.9076 (tttt) cc_final: 0.8624 (ttpp) REVERT: I 72 ASP cc_start: 0.8375 (t0) cc_final: 0.7909 (t0) REVERT: I 77 THR cc_start: 0.9021 (m) cc_final: 0.8354 (p) REVERT: I 86 ASP cc_start: 0.8304 (m-30) cc_final: 0.7919 (m-30) REVERT: I 97 TYR cc_start: 0.9122 (t80) cc_final: 0.8833 (t80) REVERT: I 154 TRP cc_start: 0.8435 (m100) cc_final: 0.7902 (m100) REVERT: I 161 SER cc_start: 0.8234 (m) cc_final: 0.7885 (p) REVERT: I 214 LYS cc_start: 0.8346 (mttt) cc_final: 0.7875 (tptt) REVERT: L 79 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7372 (mt-10) REVERT: L 82 ASP cc_start: 0.8778 (m-30) cc_final: 0.8412 (m-30) REVERT: L 118 PHE cc_start: 0.8541 (m-80) cc_final: 0.7705 (m-80) REVERT: L 124 GLN cc_start: 0.7752 (tt0) cc_final: 0.7083 (tt0) REVERT: M 24 ARG cc_start: 0.8499 (ttm110) cc_final: 0.8190 (ttp80) REVERT: M 79 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7377 (mt-10) REVERT: M 82 ASP cc_start: 0.8785 (m-30) cc_final: 0.8437 (m-30) REVERT: M 118 PHE cc_start: 0.8236 (m-80) cc_final: 0.7390 (m-80) REVERT: M 124 GLN cc_start: 0.7528 (tt0) cc_final: 0.7014 (tt0) REVERT: M 126 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7664 (tppt) REVERT: M 161 GLU cc_start: 0.8268 (pt0) cc_final: 0.8010 (pp20) outliers start: 43 outliers final: 32 residues processed: 238 average time/residue: 0.1854 time to fit residues: 62.7424 Evaluate side-chains 235 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 138 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 57 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 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 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: 2.9990 chunk 99 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107242 restraints weight = 15829.360| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.43 r_work: 0.3170 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9582 Z= 0.254 Angle : 0.618 10.099 13058 Z= 0.311 Chirality : 0.043 0.169 1490 Planarity : 0.005 0.046 1608 Dihedral : 7.329 58.657 1710 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.91 % Allowed : 16.02 % Favored : 80.08 % 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: 1.25 (0.24), residues: 1192 helix: 1.34 (0.33), residues: 246 sheet: 1.81 (0.26), residues: 384 loop : -0.07 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 89 HIS 0.002 0.001 HIS C 145 PHE 0.015 0.001 PHE C 62 TYR 0.038 0.002 TYR C 94 ARG 0.002 0.000 ARG L 211 *********************** 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 245 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8735 (OUTLIER) cc_final: 0.7330 (p90) REVERT: D 116 LYS cc_start: 0.8427 (mttt) cc_final: 0.7891 (mttt) REVERT: D 137 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: H 5 GLN cc_start: 0.8547 (tt0) cc_final: 0.8116 (tp40) REVERT: H 64 LYS cc_start: 0.9046 (tttt) cc_final: 0.8612 (ttpp) REVERT: H 72 ASP cc_start: 0.8214 (t0) cc_final: 0.7695 (t0) REVERT: H 77 THR cc_start: 0.8975 (m) cc_final: 0.8367 (p) REVERT: H 86 ASP cc_start: 0.8333 (m-30) cc_final: 0.7918 (m-30) REVERT: H 161 SER cc_start: 0.8076 (m) cc_final: 0.7744 (p) REVERT: H 207 VAL cc_start: 0.8026 (t) cc_final: 0.7815 (p) REVERT: I 64 LYS cc_start: 0.9022 (tttt) cc_final: 0.8575 (ttpp) REVERT: I 72 ASP cc_start: 0.8224 (t0) cc_final: 0.7703 (t0) REVERT: I 77 THR cc_start: 0.9007 (m) cc_final: 0.8346 (p) REVERT: I 86 ASP cc_start: 0.8270 (m-30) cc_final: 0.7856 (m-30) REVERT: I 97 TYR cc_start: 0.9024 (t80) cc_final: 0.8649 (t80) REVERT: I 154 TRP cc_start: 0.8387 (m100) cc_final: 0.7928 (m100) REVERT: I 161 SER cc_start: 0.8115 (m) cc_final: 0.7776 (p) REVERT: I 214 LYS cc_start: 0.8342 (mttt) cc_final: 0.7784 (tptt) REVERT: L 79 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7422 (mt-10) REVERT: L 82 ASP cc_start: 0.8817 (m-30) cc_final: 0.8411 (m-30) REVERT: L 118 PHE cc_start: 0.8517 (m-80) cc_final: 0.7724 (m-80) REVERT: L 124 GLN cc_start: 0.7822 (tt0) cc_final: 0.7151 (tt0) REVERT: M 24 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8077 (ttp80) REVERT: M 79 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7315 (mt-10) REVERT: M 82 ASP cc_start: 0.8841 (m-30) cc_final: 0.8440 (m-30) REVERT: M 118 PHE cc_start: 0.8289 (m-80) cc_final: 0.7546 (m-80) REVERT: M 124 GLN cc_start: 0.7524 (tt0) cc_final: 0.6946 (tt0) REVERT: M 126 LYS cc_start: 0.8031 (mtmt) cc_final: 0.7655 (tppt) REVERT: M 161 GLU cc_start: 0.8311 (pt0) cc_final: 0.8028 (pp20) outliers start: 40 outliers final: 29 residues processed: 235 average time/residue: 0.1880 time to fit residues: 62.9419 Evaluate side-chains 225 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 137 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.159902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109812 restraints weight = 15787.917| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.45 r_work: 0.3202 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9582 Z= 0.158 Angle : 0.564 10.207 13058 Z= 0.281 Chirality : 0.042 0.138 1490 Planarity : 0.004 0.044 1608 Dihedral : 7.101 57.780 1710 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.22 % Allowed : 16.70 % Favored : 80.08 % 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: 1.33 (0.25), residues: 1192 helix: 1.35 (0.33), residues: 258 sheet: 1.79 (0.26), residues: 396 loop : -0.02 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.001 0.000 HIS L 198 PHE 0.011 0.001 PHE I 122 TYR 0.045 0.001 TYR C 94 ARG 0.001 0.000 ARG D 109 *********************** 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 245 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8590 (OUTLIER) cc_final: 0.7183 (p90) REVERT: C 116 LYS cc_start: 0.8618 (mttt) cc_final: 0.8246 (mmmt) REVERT: C 204 GLN cc_start: 0.9156 (tp40) cc_final: 0.8729 (tp40) REVERT: D 89 TRP cc_start: 0.8586 (OUTLIER) cc_final: 0.7324 (p90) REVERT: D 116 LYS cc_start: 0.8363 (mttt) cc_final: 0.7819 (mttt) REVERT: H 5 GLN cc_start: 0.8530 (tt0) cc_final: 0.8121 (tp40) REVERT: H 64 LYS cc_start: 0.8856 (tttt) cc_final: 0.8404 (ttpp) REVERT: H 72 ASP cc_start: 0.8131 (t0) cc_final: 0.7574 (t0) REVERT: H 77 THR cc_start: 0.8945 (m) cc_final: 0.8429 (p) REVERT: H 86 ASP cc_start: 0.8258 (m-30) cc_final: 0.7821 (m-30) REVERT: H 161 SER cc_start: 0.8024 (m) cc_final: 0.7708 (p) REVERT: H 207 VAL cc_start: 0.7948 (t) cc_final: 0.7724 (p) REVERT: I 64 LYS cc_start: 0.8855 (tttt) cc_final: 0.8405 (ttpp) REVERT: I 72 ASP cc_start: 0.8182 (t0) cc_final: 0.7636 (t0) REVERT: I 77 THR cc_start: 0.8954 (m) cc_final: 0.8409 (p) REVERT: I 97 TYR cc_start: 0.8926 (t80) cc_final: 0.8481 (t80) REVERT: I 154 TRP cc_start: 0.8420 (m100) cc_final: 0.8019 (m100) REVERT: I 161 SER cc_start: 0.8076 (m) cc_final: 0.7726 (p) REVERT: I 214 LYS cc_start: 0.8405 (mttt) cc_final: 0.7842 (tptt) REVERT: L 79 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7362 (mt-10) REVERT: L 82 ASP cc_start: 0.8800 (m-30) cc_final: 0.8454 (m-30) REVERT: L 118 PHE cc_start: 0.8632 (m-80) cc_final: 0.7858 (m-80) REVERT: L 124 GLN cc_start: 0.7798 (tt0) cc_final: 0.7112 (tt0) REVERT: M 24 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8076 (ttp80) REVERT: M 79 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7403 (mt-10) REVERT: M 82 ASP cc_start: 0.8798 (m-30) cc_final: 0.8467 (m-30) REVERT: M 118 PHE cc_start: 0.8438 (m-80) cc_final: 0.7736 (m-80) REVERT: M 124 GLN cc_start: 0.7636 (tt0) cc_final: 0.6967 (tt0) REVERT: M 126 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7675 (tppt) REVERT: M 161 GLU cc_start: 0.8311 (pt0) cc_final: 0.8050 (pp20) outliers start: 33 outliers final: 25 residues processed: 233 average time/residue: 0.2174 time to fit residues: 71.7486 Evaluate side-chains 230 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 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 D residue 207 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain 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 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 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: 9.9990 chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.160153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109830 restraints weight = 16008.996| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.49 r_work: 0.3175 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9582 Z= 0.161 Angle : 0.578 12.060 13058 Z= 0.284 Chirality : 0.041 0.136 1490 Planarity : 0.004 0.046 1608 Dihedral : 7.020 55.384 1710 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.03 % Allowed : 18.16 % Favored : 78.81 % 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: 1.51 (0.25), residues: 1192 helix: 1.66 (0.34), residues: 250 sheet: 1.87 (0.26), residues: 394 loop : 0.08 (0.28), residues: 548 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 0.011 0.001 PHE D 62 TYR 0.039 0.002 TYR C 94 ARG 0.003 0.000 ARG L 211 *********************** 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 240 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8550 (OUTLIER) cc_final: 0.7165 (p90) REVERT: C 94 TYR cc_start: 0.9361 (m-80) cc_final: 0.9146 (m-80) REVERT: C 116 LYS cc_start: 0.8571 (mttt) cc_final: 0.8201 (mmmt) REVERT: C 197 MET cc_start: 0.9554 (ttm) cc_final: 0.9141 (tpp) REVERT: C 204 GLN cc_start: 0.9067 (tp40) cc_final: 0.8590 (tp40) REVERT: D 89 TRP cc_start: 0.8526 (OUTLIER) cc_final: 0.7206 (p90) REVERT: D 116 LYS cc_start: 0.8378 (mttt) cc_final: 0.7853 (mttt) REVERT: H 5 GLN cc_start: 0.8538 (tt0) cc_final: 0.8119 (tp40) REVERT: H 64 LYS cc_start: 0.8861 (tttt) cc_final: 0.8407 (ttpp) REVERT: H 72 ASP cc_start: 0.8099 (t0) cc_final: 0.7514 (t0) REVERT: H 77 THR cc_start: 0.8938 (m) cc_final: 0.8431 (p) REVERT: H 86 ASP cc_start: 0.8251 (m-30) cc_final: 0.7844 (m-30) REVERT: H 161 SER cc_start: 0.8085 (m) cc_final: 0.7730 (p) REVERT: H 198 VAL cc_start: 0.8921 (t) cc_final: 0.8625 (m) REVERT: I 64 LYS cc_start: 0.8858 (tttt) cc_final: 0.8403 (ttpp) REVERT: I 72 ASP cc_start: 0.8123 (t0) cc_final: 0.7538 (t0) REVERT: I 77 THR cc_start: 0.8956 (m) cc_final: 0.8429 (p) REVERT: I 97 TYR cc_start: 0.8934 (t80) cc_final: 0.8399 (t80) REVERT: I 154 TRP cc_start: 0.8402 (m100) cc_final: 0.7985 (m100) REVERT: I 161 SER cc_start: 0.8152 (m) cc_final: 0.7837 (p) REVERT: I 214 LYS cc_start: 0.8403 (mttt) cc_final: 0.7834 (tptt) REVERT: L 79 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7337 (mt-10) REVERT: L 82 ASP cc_start: 0.8819 (m-30) cc_final: 0.8466 (m-30) REVERT: L 118 PHE cc_start: 0.8546 (m-80) cc_final: 0.7841 (m-80) REVERT: L 124 GLN cc_start: 0.7767 (tt0) cc_final: 0.7097 (tt0) REVERT: M 24 ARG cc_start: 0.8400 (ttm110) cc_final: 0.8073 (ttp80) REVERT: M 79 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7361 (mt-10) REVERT: M 82 ASP cc_start: 0.8779 (m-30) cc_final: 0.8444 (m-30) REVERT: M 118 PHE cc_start: 0.8390 (m-80) cc_final: 0.7733 (m-80) REVERT: M 124 GLN cc_start: 0.7443 (tt0) cc_final: 0.6984 (tt0) REVERT: M 161 GLU cc_start: 0.8263 (pt0) cc_final: 0.7989 (pp20) REVERT: M 167 ASP cc_start: 0.7642 (t70) cc_final: 0.7306 (t70) outliers start: 31 outliers final: 24 residues processed: 231 average time/residue: 0.2471 time to fit residues: 82.1845 Evaluate side-chains 227 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 95 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 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 D residue 207 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain 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 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: 1.9990 chunk 98 optimal weight: 0.0050 chunk 51 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.161507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112090 restraints weight = 16042.163| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.60 r_work: 0.3245 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9582 Z= 0.125 Angle : 0.570 12.274 13058 Z= 0.274 Chirality : 0.041 0.134 1490 Planarity : 0.004 0.044 1608 Dihedral : 6.830 56.572 1710 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.34 % Allowed : 19.14 % Favored : 78.52 % 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: 1.51 (0.25), residues: 1192 helix: 1.58 (0.33), residues: 254 sheet: 1.92 (0.25), residues: 390 loop : 0.07 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.005 0.001 HIS C 63 PHE 0.010 0.001 PHE D 62 TYR 0.035 0.001 TYR C 94 ARG 0.002 0.000 ARG H 94 *********************** 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 239 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8388 (OUTLIER) cc_final: 0.7191 (p90) REVERT: C 94 TYR cc_start: 0.9330 (m-80) cc_final: 0.9086 (m-80) REVERT: C 116 LYS cc_start: 0.8527 (mttt) cc_final: 0.8172 (mmmt) REVERT: C 197 MET cc_start: 0.9567 (ttm) cc_final: 0.9099 (tpp) REVERT: C 204 GLN cc_start: 0.8922 (tp40) cc_final: 0.8483 (tp40) REVERT: D 89 TRP cc_start: 0.8518 (OUTLIER) cc_final: 0.7319 (p90) REVERT: D 116 LYS cc_start: 0.8346 (mttt) cc_final: 0.7838 (mttt) REVERT: H 5 GLN cc_start: 0.8593 (tt0) cc_final: 0.8223 (tp40) REVERT: H 64 LYS cc_start: 0.8743 (tttt) cc_final: 0.8319 (ttpp) REVERT: H 77 THR cc_start: 0.8943 (m) cc_final: 0.8530 (p) REVERT: H 161 SER cc_start: 0.8084 (m) cc_final: 0.7731 (p) REVERT: H 195 ILE cc_start: 0.6293 (mt) cc_final: 0.5938 (tp) REVERT: H 198 VAL cc_start: 0.8905 (t) cc_final: 0.8638 (m) REVERT: I 64 LYS cc_start: 0.8716 (tttt) cc_final: 0.8295 (ttpp) REVERT: I 72 ASP cc_start: 0.8104 (t0) cc_final: 0.7515 (t0) REVERT: I 77 THR cc_start: 0.8957 (m) cc_final: 0.8518 (p) REVERT: I 97 TYR cc_start: 0.8818 (t80) cc_final: 0.8481 (t80) REVERT: I 98 TYR cc_start: 0.8466 (t80) cc_final: 0.8164 (t80) REVERT: I 154 TRP cc_start: 0.8383 (m100) cc_final: 0.8118 (m100) REVERT: I 161 SER cc_start: 0.8155 (m) cc_final: 0.7850 (p) REVERT: I 214 LYS cc_start: 0.8489 (mttt) cc_final: 0.7941 (tptt) REVERT: L 79 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7323 (mt-10) REVERT: L 82 ASP cc_start: 0.8813 (m-30) cc_final: 0.8537 (m-30) REVERT: L 118 PHE cc_start: 0.8597 (m-80) cc_final: 0.8089 (m-80) REVERT: L 124 GLN cc_start: 0.7857 (tt0) cc_final: 0.7138 (tt0) REVERT: L 211 ARG cc_start: 0.7280 (ptm-80) cc_final: 0.7009 (ptm-80) REVERT: M 24 ARG cc_start: 0.8391 (ttm110) cc_final: 0.8073 (ttp80) REVERT: M 79 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7378 (mt-10) REVERT: M 82 ASP cc_start: 0.8733 (m-30) cc_final: 0.8420 (m-30) REVERT: M 118 PHE cc_start: 0.8378 (m-80) cc_final: 0.7813 (m-80) REVERT: M 124 GLN cc_start: 0.7481 (tt0) cc_final: 0.6855 (tt0) REVERT: M 161 GLU cc_start: 0.8259 (pt0) cc_final: 0.7988 (pp20) REVERT: M 167 ASP cc_start: 0.7568 (t70) cc_final: 0.7285 (t0) outliers start: 24 outliers final: 17 residues processed: 229 average time/residue: 0.1771 time to fit residues: 58.3740 Evaluate side-chains 212 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain D residue 63 HIS Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.160069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109949 restraints weight = 15814.084| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.56 r_work: 0.3221 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9582 Z= 0.172 Angle : 0.609 12.825 13058 Z= 0.292 Chirality : 0.041 0.157 1490 Planarity : 0.005 0.047 1608 Dihedral : 6.813 55.814 1710 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.25 % Allowed : 19.63 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.49 (0.25), residues: 1192 helix: 1.53 (0.33), residues: 254 sheet: 1.95 (0.25), residues: 390 loop : 0.05 (0.28), residues: 548 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 0.014 0.001 PHE D 62 TYR 0.036 0.001 TYR C 94 ARG 0.002 0.000 ARG L 211 *********************** 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 222 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8471 (OUTLIER) cc_final: 0.7326 (p90) REVERT: C 116 LYS cc_start: 0.8574 (mttt) cc_final: 0.8250 (mmmt) REVERT: C 197 MET cc_start: 0.9581 (ttm) cc_final: 0.9133 (tpp) REVERT: C 204 GLN cc_start: 0.8967 (tp40) cc_final: 0.8572 (tp40) REVERT: D 89 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.7221 (p90) REVERT: D 116 LYS cc_start: 0.8453 (mttt) cc_final: 0.7965 (mttt) REVERT: H 5 GLN cc_start: 0.8613 (tt0) cc_final: 0.8241 (tp40) REVERT: H 64 LYS cc_start: 0.8904 (tttt) cc_final: 0.8456 (ttpp) REVERT: H 77 THR cc_start: 0.8963 (m) cc_final: 0.8523 (p) REVERT: H 154 TRP cc_start: 0.8123 (m100) cc_final: 0.7811 (m100) REVERT: H 161 SER cc_start: 0.8088 (m) cc_final: 0.7819 (p) REVERT: H 198 VAL cc_start: 0.8910 (t) cc_final: 0.8661 (m) REVERT: I 64 LYS cc_start: 0.8821 (tttt) cc_final: 0.8365 (ttpp) REVERT: I 77 THR cc_start: 0.8973 (m) cc_final: 0.8513 (p) REVERT: I 97 TYR cc_start: 0.8928 (t80) cc_final: 0.8448 (t80) REVERT: I 98 TYR cc_start: 0.8568 (t80) cc_final: 0.8241 (t80) REVERT: I 154 TRP cc_start: 0.8355 (m100) cc_final: 0.8079 (m100) REVERT: I 161 SER cc_start: 0.8200 (m) cc_final: 0.7897 (p) REVERT: I 214 LYS cc_start: 0.8469 (mttt) cc_final: 0.7930 (tptt) REVERT: L 79 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7355 (mt-10) REVERT: L 82 ASP cc_start: 0.8802 (m-30) cc_final: 0.8497 (m-30) REVERT: L 118 PHE cc_start: 0.8530 (m-80) cc_final: 0.8029 (m-80) REVERT: L 124 GLN cc_start: 0.7800 (tt0) cc_final: 0.7134 (tt0) REVERT: L 161 GLU cc_start: 0.8031 (pp20) cc_final: 0.7756 (pp20) REVERT: L 211 ARG cc_start: 0.7195 (ptm-80) cc_final: 0.6878 (ptm-80) REVERT: M 24 ARG cc_start: 0.8412 (ttm110) cc_final: 0.8075 (ttp80) REVERT: M 79 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7375 (mt-10) REVERT: M 82 ASP cc_start: 0.8730 (m-30) cc_final: 0.8412 (m-30) REVERT: M 118 PHE cc_start: 0.8395 (m-80) cc_final: 0.7844 (m-80) REVERT: M 124 GLN cc_start: 0.7449 (tt0) cc_final: 0.6987 (tt0) REVERT: M 167 ASP cc_start: 0.7574 (t70) cc_final: 0.7277 (t70) outliers start: 23 outliers final: 18 residues processed: 214 average time/residue: 0.1840 time to fit residues: 56.8587 Evaluate side-chains 212 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain 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 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: 2.9990 chunk 7 optimal weight: 7.9990 chunk 32 optimal weight: 0.1980 chunk 114 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.159178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108912 restraints weight = 15995.186| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.59 r_work: 0.3203 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9582 Z= 0.205 Angle : 0.626 13.268 13058 Z= 0.302 Chirality : 0.042 0.156 1490 Planarity : 0.005 0.045 1608 Dihedral : 6.848 56.423 1710 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.34 % Allowed : 19.34 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.25), residues: 1192 helix: 1.40 (0.33), residues: 254 sheet: 1.96 (0.25), residues: 392 loop : 0.02 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 89 HIS 0.001 0.000 HIS M 34 PHE 0.015 0.001 PHE D 62 TYR 0.040 0.002 TYR C 94 ARG 0.002 0.000 ARG L 211 ********************** 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 217 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8467 (OUTLIER) cc_final: 0.7276 (p90) REVERT: C 116 LYS cc_start: 0.8627 (mttt) cc_final: 0.8300 (mmmt) REVERT: C 204 GLN cc_start: 0.8964 (tp40) cc_final: 0.8563 (tp40) REVERT: D 89 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.6936 (p90) REVERT: D 116 LYS cc_start: 0.8456 (mttt) cc_final: 0.7999 (mttt) REVERT: D 197 MET cc_start: 0.9491 (ttm) cc_final: 0.9169 (tpp) REVERT: H 5 GLN cc_start: 0.8604 (tt0) cc_final: 0.8217 (tp40) REVERT: H 64 LYS cc_start: 0.8936 (tttt) cc_final: 0.8496 (ttpp) REVERT: H 77 THR cc_start: 0.8976 (m) cc_final: 0.8499 (p) REVERT: H 161 SER cc_start: 0.8264 (m) cc_final: 0.7949 (p) REVERT: H 198 VAL cc_start: 0.8955 (t) cc_final: 0.8705 (m) REVERT: I 64 LYS cc_start: 0.8917 (tttt) cc_final: 0.8504 (ttpp) REVERT: I 72 ASP cc_start: 0.8235 (t0) cc_final: 0.7659 (t0) REVERT: I 77 THR cc_start: 0.9030 (m) cc_final: 0.8527 (p) REVERT: I 97 TYR cc_start: 0.9014 (t80) cc_final: 0.8572 (t80) REVERT: I 154 TRP cc_start: 0.8450 (m100) cc_final: 0.8030 (m100) REVERT: I 161 SER cc_start: 0.8295 (m) cc_final: 0.8007 (p) REVERT: I 214 LYS cc_start: 0.8485 (mttt) cc_final: 0.7931 (tptt) REVERT: L 79 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7427 (mt-10) REVERT: L 82 ASP cc_start: 0.8778 (m-30) cc_final: 0.8480 (m-30) REVERT: L 118 PHE cc_start: 0.8600 (m-80) cc_final: 0.8127 (m-80) REVERT: L 124 GLN cc_start: 0.7833 (tt0) cc_final: 0.7128 (tt0) REVERT: L 161 GLU cc_start: 0.8049 (pp20) cc_final: 0.7733 (pp20) REVERT: L 211 ARG cc_start: 0.7202 (ptm-80) cc_final: 0.6873 (ptm-80) REVERT: M 24 ARG cc_start: 0.8406 (ttm110) cc_final: 0.8081 (ttp80) REVERT: M 79 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7462 (mt-10) REVERT: M 82 ASP cc_start: 0.8713 (m-30) cc_final: 0.8432 (m-30) REVERT: M 118 PHE cc_start: 0.8420 (m-80) cc_final: 0.7884 (m-80) REVERT: M 124 GLN cc_start: 0.7448 (tt0) cc_final: 0.6933 (tt0) REVERT: M 161 GLU cc_start: 0.8225 (pt0) cc_final: 0.7914 (pp20) REVERT: M 167 ASP cc_start: 0.7620 (t70) cc_final: 0.7335 (t70) outliers start: 24 outliers final: 21 residues processed: 208 average time/residue: 0.2326 time to fit residues: 69.5792 Evaluate side-chains 214 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 208 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 71 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 77 optimal weight: 0.0670 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 59 optimal weight: 0.0980 chunk 29 optimal weight: 0.0870 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.164086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114504 restraints weight = 15858.109| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.53 r_work: 0.3290 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9582 Z= 0.129 Angle : 0.588 13.345 13058 Z= 0.279 Chirality : 0.041 0.151 1490 Planarity : 0.004 0.044 1608 Dihedral : 6.628 57.783 1710 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.15 % Allowed : 20.21 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.49 (0.34), residues: 254 sheet: 1.91 (0.25), residues: 392 loop : 0.21 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.002 0.000 HIS H 35 PHE 0.014 0.001 PHE D 203 TYR 0.037 0.001 TYR C 94 ARG 0.003 0.000 ARG L 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4992.64 seconds wall clock time: 88 minutes 28.73 seconds (5308.73 seconds total)