Starting phenix.real_space_refine on Fri Feb 14 00:44:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vja_21212/02_2025/6vja_21212.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vja_21212/02_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_21212/02_2025/6vja_21212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vja_21212/02_2025/6vja_21212.map" model { file = "/net/cci-nas-00/data/ceres_data/6vja_21212/02_2025/6vja_21212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vja_21212/02_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-5592/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: 6.08, per 1000 atoms: 0.65 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 22 sheets defined 27.6% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 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: 2.91 Time building geometry restraints manager: 2.41 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.910 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.020 ------------------------------------------------------------------------------- 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 : 1.030 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: 0.2053 time to fit residues: 87.1667 Evaluate side-chains 226 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain D residue 89 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 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: 1.1786 ------------------------------------------------------------------------------- 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 L 53 ASN L 124 GLN M 53 ASN M 124 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.159109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109816 restraints weight = 15961.539| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.52 r_work: 0.3218 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9582 Z= 0.185 Angle : 0.649 8.552 13058 Z= 0.330 Chirality : 0.044 0.210 1490 Planarity : 0.004 0.044 1608 Dihedral : 7.661 59.910 1710 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.66 % Allowed : 11.04 % 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: 1.66 (0.24), residues: 1192 helix: 1.04 (0.33), residues: 248 sheet: 2.14 (0.25), residues: 404 loop : 0.39 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 89 HIS 0.003 0.001 HIS D 145 PHE 0.016 0.001 PHE I 122 TYR 0.026 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 281 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 264 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8552 (mttt) cc_final: 0.8140 (mmmt) REVERT: C 139 LEU cc_start: 0.8988 (mm) cc_final: 0.8728 (mm) REVERT: C 175 LYS cc_start: 0.8582 (mmtp) cc_final: 0.8345 (mmtp) REVERT: D 62 PHE cc_start: 0.8714 (t80) cc_final: 0.8387 (t80) REVERT: D 89 TRP cc_start: 0.8746 (OUTLIER) cc_final: 0.7629 (p90) REVERT: D 116 LYS cc_start: 0.8234 (mttt) cc_final: 0.7669 (mttt) REVERT: D 175 LYS cc_start: 0.8626 (mmtp) cc_final: 0.8366 (mmtp) REVERT: H 5 GLN cc_start: 0.8613 (tt0) cc_final: 0.8203 (tp40) REVERT: H 64 LYS cc_start: 0.8765 (tttt) cc_final: 0.8356 (ttpp) REVERT: H 72 ASP cc_start: 0.8229 (t0) cc_final: 0.7711 (t0) REVERT: H 77 THR cc_start: 0.8922 (m) cc_final: 0.8319 (p) REVERT: H 85 GLU cc_start: 0.9166 (tp30) cc_final: 0.8878 (tp30) REVERT: H 86 ASP cc_start: 0.8427 (m-30) cc_final: 0.8155 (m-30) REVERT: H 154 TRP cc_start: 0.8174 (m100) cc_final: 0.7779 (m100) REVERT: I 5 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: I 64 LYS cc_start: 0.8830 (tttt) cc_final: 0.8421 (ttpp) REVERT: I 72 ASP cc_start: 0.8188 (t0) cc_final: 0.7739 (t0) REVERT: I 77 THR cc_start: 0.8922 (m) cc_final: 0.8308 (p) REVERT: I 86 ASP cc_start: 0.8324 (m-30) cc_final: 0.7964 (m-30) REVERT: I 122 PHE cc_start: 0.7247 (m-10) cc_final: 0.6971 (m-10) REVERT: I 154 TRP cc_start: 0.8129 (m100) cc_final: 0.7705 (m100) REVERT: I 161 SER cc_start: 0.8141 (m) cc_final: 0.7743 (p) REVERT: I 195 ILE cc_start: 0.7950 (mt) cc_final: 0.7477 (tt) REVERT: I 214 LYS cc_start: 0.8474 (mttt) cc_final: 0.7982 (tptt) REVERT: L 24 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7907 (ttp80) REVERT: L 79 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7163 (mt-10) REVERT: L 82 ASP cc_start: 0.8787 (m-30) cc_final: 0.8457 (m-30) REVERT: L 118 PHE cc_start: 0.8624 (m-80) cc_final: 0.7807 (m-80) REVERT: L 124 GLN cc_start: 0.7928 (tt0) cc_final: 0.7336 (tt0) REVERT: M 24 ARG cc_start: 0.8436 (ttm110) cc_final: 0.8114 (ttp80) REVERT: M 79 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7217 (mt-10) REVERT: M 82 ASP cc_start: 0.8794 (m-30) cc_final: 0.8462 (m-30) REVERT: M 118 PHE cc_start: 0.8559 (m-80) cc_final: 0.7771 (m-80) REVERT: M 124 GLN cc_start: 0.7832 (tt0) cc_final: 0.7438 (tt0) outliers start: 17 outliers final: 10 residues processed: 275 average time/residue: 0.2065 time to fit residues: 80.0822 Evaluate side-chains 226 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain 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: 0.9990 chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN D 181 GLN L 160 GLN M 160 GLN M 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.159063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108218 restraints weight = 16059.947| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.59 r_work: 0.3195 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9582 Z= 0.242 Angle : 0.631 7.971 13058 Z= 0.319 Chirality : 0.043 0.221 1490 Planarity : 0.005 0.047 1608 Dihedral : 7.406 54.744 1710 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.91 % Allowed : 13.28 % 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: 1.71 (0.25), residues: 1192 helix: 1.34 (0.34), residues: 246 sheet: 2.12 (0.26), residues: 370 loop : 0.46 (0.27), 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 0.015 0.002 PHE H 100D TYR 0.027 0.002 TYR H 100C ARG 0.005 0.000 ARG M 211 *********************** 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 265 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8501 (mttt) cc_final: 0.8286 (mmmt) REVERT: C 137 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8008 (m-30) REVERT: C 148 LYS cc_start: 0.7233 (ptmt) cc_final: 0.6992 (ptmt) REVERT: D 62 PHE cc_start: 0.8699 (t80) cc_final: 0.8313 (t80) REVERT: D 116 LYS cc_start: 0.8403 (mttt) cc_final: 0.7838 (mttt) REVERT: H 5 GLN cc_start: 0.8663 (tt0) cc_final: 0.8272 (tp40) REVERT: H 64 LYS cc_start: 0.8954 (tttt) cc_final: 0.8533 (ttpp) REVERT: H 72 ASP cc_start: 0.8352 (t0) cc_final: 0.7861 (t0) REVERT: H 77 THR cc_start: 0.9010 (m) cc_final: 0.8475 (p) REVERT: H 85 GLU cc_start: 0.9087 (tp30) cc_final: 0.8866 (tp30) REVERT: H 86 ASP cc_start: 0.8451 (m-30) cc_final: 0.8095 (m-30) REVERT: H 154 TRP cc_start: 0.8388 (m100) cc_final: 0.7939 (m100) REVERT: I 64 LYS cc_start: 0.8976 (tttt) cc_final: 0.8543 (ttpp) REVERT: I 72 ASP cc_start: 0.8422 (t0) cc_final: 0.7962 (t0) REVERT: I 77 THR cc_start: 0.9012 (m) cc_final: 0.8462 (p) REVERT: I 86 ASP cc_start: 0.8377 (m-30) cc_final: 0.7932 (m-30) REVERT: I 154 TRP cc_start: 0.8354 (m100) cc_final: 0.7806 (m100) REVERT: I 161 SER cc_start: 0.8271 (m) cc_final: 0.7949 (p) REVERT: I 214 LYS cc_start: 0.8512 (mttt) cc_final: 0.7959 (tptt) REVERT: L 79 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7224 (mt-10) REVERT: L 82 ASP cc_start: 0.8693 (m-30) cc_final: 0.8433 (m-30) REVERT: L 118 PHE cc_start: 0.8549 (m-80) cc_final: 0.7851 (m-80) REVERT: L 124 GLN cc_start: 0.7896 (tt0) cc_final: 0.7153 (tt0) REVERT: L 148 TRP cc_start: 0.6880 (m100) cc_final: 0.6662 (m100) REVERT: M 24 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8203 (ttp80) REVERT: M 79 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7302 (mt-10) REVERT: M 82 ASP cc_start: 0.8731 (m-30) cc_final: 0.8465 (m-30) REVERT: M 118 PHE cc_start: 0.8583 (m-80) cc_final: 0.7905 (m-80) REVERT: M 124 GLN cc_start: 0.7840 (tt0) cc_final: 0.7410 (tt0) REVERT: M 126 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7873 (tppt) outliers start: 40 outliers final: 31 residues processed: 251 average time/residue: 0.1913 time to fit residues: 68.5098 Evaluate side-chains 239 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 63 HIS Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain L residue 81 GLU 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 81 GLU 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: 5.9990 chunk 3 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 61 optimal weight: 0.0270 chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.3444 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.157361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107306 restraints weight = 15770.773| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.42 r_work: 0.3148 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9582 Z= 0.270 Angle : 0.624 7.475 13058 Z= 0.315 Chirality : 0.043 0.171 1490 Planarity : 0.005 0.046 1608 Dihedral : 7.328 55.602 1710 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.30 % Allowed : 14.16 % Favored : 81.54 % 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: 1.60 (0.25), residues: 1192 helix: 1.40 (0.34), residues: 246 sheet: 2.03 (0.26), residues: 384 loop : 0.26 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 89 HIS 0.003 0.001 HIS C 145 PHE 0.014 0.002 PHE C 62 TYR 0.022 0.002 TYR H 100C 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: 44 poor density : 210 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.7324 (p90) REVERT: C 116 LYS cc_start: 0.8607 (mttt) cc_final: 0.8234 (mmmt) REVERT: C 137 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: C 148 LYS cc_start: 0.7231 (ptmt) cc_final: 0.7020 (ptmt) REVERT: C 175 LYS cc_start: 0.8746 (mmtp) cc_final: 0.8494 (mmtp) REVERT: D 94 TYR cc_start: 0.9370 (m-80) cc_final: 0.9138 (m-80) REVERT: D 116 LYS cc_start: 0.8457 (mttt) cc_final: 0.7906 (mttt) REVERT: D 175 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8453 (mmtp) REVERT: D 204 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8661 (tm-30) REVERT: H 5 GLN cc_start: 0.8575 (tt0) cc_final: 0.8166 (tp40) REVERT: H 64 LYS cc_start: 0.9019 (tttt) cc_final: 0.8577 (ttpp) REVERT: H 72 ASP cc_start: 0.8240 (t0) cc_final: 0.7685 (t0) REVERT: H 77 THR cc_start: 0.8991 (m) cc_final: 0.8395 (p) REVERT: H 85 GLU cc_start: 0.9127 (tp30) cc_final: 0.8903 (tp30) REVERT: H 86 ASP cc_start: 0.8354 (m-30) cc_final: 0.7963 (m-30) REVERT: H 154 TRP cc_start: 0.8308 (m100) cc_final: 0.7918 (m100) REVERT: H 161 SER cc_start: 0.8106 (m) cc_final: 0.7751 (p) REVERT: H 195 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6395 (mm) REVERT: I 64 LYS cc_start: 0.9026 (tttt) cc_final: 0.8569 (ttpp) REVERT: I 72 ASP cc_start: 0.8291 (t0) cc_final: 0.7745 (t0) REVERT: I 77 THR cc_start: 0.9007 (m) cc_final: 0.8395 (p) REVERT: I 86 ASP cc_start: 0.8252 (m-30) cc_final: 0.7862 (m-30) REVERT: I 154 TRP cc_start: 0.8335 (m100) cc_final: 0.7834 (m100) REVERT: I 161 SER cc_start: 0.8143 (m) cc_final: 0.7789 (p) REVERT: I 214 LYS cc_start: 0.8445 (mttt) cc_final: 0.7931 (tptt) REVERT: L 79 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7222 (mt-10) REVERT: L 82 ASP cc_start: 0.8804 (m-30) cc_final: 0.8420 (m-30) REVERT: L 118 PHE cc_start: 0.8565 (m-80) cc_final: 0.7828 (m-80) REVERT: L 124 GLN cc_start: 0.7754 (tt0) cc_final: 0.7005 (tt0) REVERT: M 24 ARG cc_start: 0.8412 (ttm110) cc_final: 0.8087 (ttp80) REVERT: M 79 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7246 (mt-10) REVERT: M 82 ASP cc_start: 0.8794 (m-30) cc_final: 0.8393 (m-30) REVERT: M 118 PHE cc_start: 0.8556 (m-80) cc_final: 0.7867 (m-80) REVERT: M 124 GLN cc_start: 0.7545 (tt0) cc_final: 0.7113 (tt0) REVERT: M 126 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7794 (tppt) outliers start: 44 outliers final: 29 residues processed: 239 average time/residue: 0.1938 time to fit residues: 65.6522 Evaluate side-chains 226 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 HIS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 63 HIS Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 204 GLN 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 H residue 211 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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** H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.159067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108604 restraints weight = 15818.390| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.47 r_work: 0.3167 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9582 Z= 0.209 Angle : 0.583 6.734 13058 Z= 0.291 Chirality : 0.042 0.149 1490 Planarity : 0.005 0.045 1608 Dihedral : 7.140 58.819 1710 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.52 % Allowed : 15.62 % Favored : 80.86 % 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: 1.60 (0.25), residues: 1192 helix: 1.70 (0.34), residues: 242 sheet: 1.93 (0.25), residues: 396 loop : 0.16 (0.27), residues: 554 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 0.042 0.002 TYR C 94 ARG 0.003 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: 36 poor density : 209 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8585 (OUTLIER) cc_final: 0.7315 (p90) REVERT: C 116 LYS cc_start: 0.8604 (mttt) cc_final: 0.8219 (mmmt) REVERT: C 137 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: D 116 LYS cc_start: 0.8378 (mttt) cc_final: 0.7838 (mttt) REVERT: H 5 GLN cc_start: 0.8567 (tt0) cc_final: 0.8168 (tp40) REVERT: H 64 LYS cc_start: 0.8977 (tttt) cc_final: 0.8520 (ttpp) REVERT: H 72 ASP cc_start: 0.8184 (t0) cc_final: 0.7615 (t0) REVERT: H 77 THR cc_start: 0.8991 (m) cc_final: 0.8444 (p) REVERT: H 85 GLU cc_start: 0.9111 (tp30) cc_final: 0.8884 (tp30) REVERT: H 86 ASP cc_start: 0.8326 (m-30) cc_final: 0.7891 (m-30) REVERT: H 154 TRP cc_start: 0.8284 (m100) cc_final: 0.7942 (m100) REVERT: H 161 SER cc_start: 0.8046 (m) cc_final: 0.7701 (p) REVERT: H 195 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.5924 (mm) REVERT: I 64 LYS cc_start: 0.8976 (tttt) cc_final: 0.8515 (ttpp) REVERT: I 72 ASP cc_start: 0.8254 (t0) cc_final: 0.7692 (t0) REVERT: I 77 THR cc_start: 0.9003 (m) cc_final: 0.8430 (p) REVERT: I 86 ASP cc_start: 0.8233 (m-30) cc_final: 0.7799 (m-30) REVERT: I 154 TRP cc_start: 0.8317 (m100) cc_final: 0.7845 (m100) REVERT: I 161 SER cc_start: 0.8121 (m) cc_final: 0.7784 (p) REVERT: I 214 LYS cc_start: 0.8438 (mttt) cc_final: 0.7884 (tptt) REVERT: L 79 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7289 (mt-10) REVERT: L 82 ASP cc_start: 0.8818 (m-30) cc_final: 0.8480 (m-30) REVERT: L 118 PHE cc_start: 0.8552 (m-80) cc_final: 0.7832 (m-80) REVERT: L 124 GLN cc_start: 0.7783 (tt0) cc_final: 0.7086 (tt0) REVERT: M 24 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8089 (ttp80) REVERT: M 79 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7282 (mt-10) REVERT: M 82 ASP cc_start: 0.8777 (m-30) cc_final: 0.8384 (m-30) REVERT: M 118 PHE cc_start: 0.8552 (m-80) cc_final: 0.7932 (m-80) REVERT: M 124 GLN cc_start: 0.7525 (tt0) cc_final: 0.6897 (tt0) REVERT: M 126 LYS cc_start: 0.8057 (mtmt) cc_final: 0.7718 (tppt) outliers start: 36 outliers final: 24 residues processed: 234 average time/residue: 0.1938 time to fit residues: 64.4774 Evaluate side-chains 229 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 137 ASP Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain 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 L residue 29 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.160020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109639 restraints weight = 15879.496| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.61 r_work: 0.3216 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9582 Z= 0.145 Angle : 0.553 7.777 13058 Z= 0.274 Chirality : 0.041 0.150 1490 Planarity : 0.004 0.044 1608 Dihedral : 6.939 58.545 1710 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.61 % Allowed : 16.21 % Favored : 80.18 % 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: 1.61 (0.25), residues: 1192 helix: 1.62 (0.34), residues: 254 sheet: 1.97 (0.25), residues: 396 loop : 0.15 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.001 0.000 HIS M 34 PHE 0.010 0.001 PHE I 122 TYR 0.042 0.001 TYR C 94 ARG 0.002 0.000 ARG L 211 *********************** 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 244 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.7250 (p90) REVERT: C 116 LYS cc_start: 0.8530 (mttt) cc_final: 0.8170 (mmmt) REVERT: C 137 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: C 166 ASN cc_start: 0.8104 (t0) cc_final: 0.7903 (t0) REVERT: D 89 TRP cc_start: 0.8540 (OUTLIER) cc_final: 0.7209 (p90) REVERT: D 116 LYS cc_start: 0.8304 (mttt) cc_final: 0.7744 (mttt) REVERT: H 5 GLN cc_start: 0.8602 (tt0) cc_final: 0.8243 (tp40) REVERT: H 64 LYS cc_start: 0.8831 (tttt) cc_final: 0.8391 (ttpp) REVERT: H 72 ASP cc_start: 0.8158 (t0) cc_final: 0.7573 (t0) REVERT: H 77 THR cc_start: 0.8946 (m) cc_final: 0.8458 (p) REVERT: H 85 GLU cc_start: 0.9068 (tp30) cc_final: 0.8851 (tp30) REVERT: H 86 ASP cc_start: 0.8345 (m-30) cc_final: 0.7894 (m-30) REVERT: H 154 TRP cc_start: 0.8278 (m100) cc_final: 0.8005 (m100) REVERT: H 161 SER cc_start: 0.8086 (m) cc_final: 0.7771 (p) REVERT: H 195 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.5944 (mm) REVERT: H 210 LYS cc_start: 0.8328 (ptmt) cc_final: 0.7899 (ptmt) REVERT: H 212 GLU cc_start: 0.7914 (pm20) cc_final: 0.7667 (pm20) REVERT: I 64 LYS cc_start: 0.8801 (tttt) cc_final: 0.8356 (ttpp) REVERT: I 72 ASP cc_start: 0.8213 (t0) cc_final: 0.7639 (t0) REVERT: I 77 THR cc_start: 0.8959 (m) cc_final: 0.8459 (p) REVERT: I 97 TYR cc_start: 0.8909 (t80) cc_final: 0.8489 (t80) REVERT: I 154 TRP cc_start: 0.8286 (m100) cc_final: 0.7896 (m100) REVERT: I 161 SER cc_start: 0.8105 (m) cc_final: 0.7760 (p) REVERT: I 195 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5849 (mm) REVERT: I 214 LYS cc_start: 0.8479 (mttt) cc_final: 0.7916 (tptt) REVERT: L 79 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7332 (mt-10) REVERT: L 82 ASP cc_start: 0.8773 (m-30) cc_final: 0.8438 (m-30) REVERT: L 118 PHE cc_start: 0.8527 (m-80) cc_final: 0.7969 (m-80) REVERT: L 124 GLN cc_start: 0.7752 (tt0) cc_final: 0.7070 (tt0) REVERT: L 165 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8779 (tp30) REVERT: L 211 ARG cc_start: 0.7355 (ptm-80) cc_final: 0.7037 (ptm-80) REVERT: M 24 ARG cc_start: 0.8425 (ttm110) cc_final: 0.8116 (ttp80) REVERT: M 79 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7318 (mt-10) REVERT: M 82 ASP cc_start: 0.8727 (m-30) cc_final: 0.8410 (m-30) REVERT: M 118 PHE cc_start: 0.8570 (m-80) cc_final: 0.8034 (m-80) REVERT: M 124 GLN cc_start: 0.7573 (tt0) cc_final: 0.6945 (tt0) REVERT: M 126 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7678 (tppt) outliers start: 37 outliers final: 23 residues processed: 228 average time/residue: 0.1948 time to fit residues: 63.7008 Evaluate side-chains 232 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS 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 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 195 ILE Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.160182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109835 restraints weight = 15967.640| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.61 r_work: 0.3214 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9582 Z= 0.154 Angle : 0.566 12.066 13058 Z= 0.276 Chirality : 0.041 0.152 1490 Planarity : 0.004 0.046 1608 Dihedral : 6.866 56.015 1710 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.12 % Allowed : 17.68 % Favored : 79.20 % 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 (0.25), residues: 1192 helix: 1.62 (0.34), residues: 254 sheet: 1.99 (0.25), residues: 394 loop : 0.18 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.001 0.000 HIS M 34 PHE 0.010 0.001 PHE I 122 TYR 0.044 0.001 TYR C 94 ARG 0.002 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: 32 poor density : 208 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8392 (OUTLIER) cc_final: 0.7144 (p90) REVERT: C 116 LYS cc_start: 0.8548 (mttt) cc_final: 0.8194 (mmmt) REVERT: C 137 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: C 166 ASN cc_start: 0.8169 (t0) cc_final: 0.7908 (t0) REVERT: D 89 TRP cc_start: 0.8514 (OUTLIER) cc_final: 0.7251 (p90) REVERT: D 116 LYS cc_start: 0.8325 (mttt) cc_final: 0.7775 (mttt) REVERT: H 5 GLN cc_start: 0.8606 (tt0) cc_final: 0.8256 (tp40) REVERT: H 64 LYS cc_start: 0.8922 (tttt) cc_final: 0.8482 (ttpp) REVERT: H 72 ASP cc_start: 0.8161 (t0) cc_final: 0.7564 (t0) REVERT: H 77 THR cc_start: 0.8964 (m) cc_final: 0.8492 (p) REVERT: H 85 GLU cc_start: 0.9060 (tp30) cc_final: 0.8839 (tp30) REVERT: H 86 ASP cc_start: 0.8341 (m-30) cc_final: 0.7866 (m-30) REVERT: H 154 TRP cc_start: 0.8271 (m100) cc_final: 0.8002 (m100) REVERT: H 161 SER cc_start: 0.8146 (m) cc_final: 0.7792 (p) REVERT: H 195 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.5916 (mm) REVERT: H 210 LYS cc_start: 0.8318 (ptmt) cc_final: 0.7841 (ptmt) REVERT: H 212 GLU cc_start: 0.7911 (pm20) cc_final: 0.7662 (pm20) REVERT: I 64 LYS cc_start: 0.8863 (tttt) cc_final: 0.8444 (ttpp) REVERT: I 72 ASP cc_start: 0.8208 (t0) cc_final: 0.7614 (t0) REVERT: I 77 THR cc_start: 0.8965 (m) cc_final: 0.8472 (p) REVERT: I 154 TRP cc_start: 0.8262 (m100) cc_final: 0.7912 (m100) REVERT: I 161 SER cc_start: 0.8141 (m) cc_final: 0.7816 (p) REVERT: I 195 ILE cc_start: 0.6343 (OUTLIER) cc_final: 0.6052 (mm) REVERT: I 214 LYS cc_start: 0.8473 (mttt) cc_final: 0.7921 (tptt) REVERT: L 79 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7355 (mt-10) REVERT: L 82 ASP cc_start: 0.8772 (m-30) cc_final: 0.8442 (m-30) REVERT: L 118 PHE cc_start: 0.8519 (m-80) cc_final: 0.8044 (m-80) REVERT: L 124 GLN cc_start: 0.7795 (tt0) cc_final: 0.7126 (tt0) REVERT: L 211 ARG cc_start: 0.7415 (ptm-80) cc_final: 0.7073 (ptm-80) REVERT: M 24 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8069 (ttp80) REVERT: M 79 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7286 (mt-10) REVERT: M 82 ASP cc_start: 0.8717 (m-30) cc_final: 0.8394 (m-30) REVERT: M 118 PHE cc_start: 0.8551 (m-80) cc_final: 0.7999 (m-80) REVERT: M 124 GLN cc_start: 0.7576 (tt0) cc_final: 0.6924 (tt0) REVERT: M 126 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7664 (tppt) outliers start: 32 outliers final: 26 residues processed: 229 average time/residue: 0.1897 time to fit residues: 62.5207 Evaluate side-chains 232 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS 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 H residue 196 CYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.157953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107816 restraints weight = 16093.850| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.51 r_work: 0.3191 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4213 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= 0.207 Angle : 0.592 11.502 13058 Z= 0.290 Chirality : 0.042 0.155 1490 Planarity : 0.005 0.046 1608 Dihedral : 6.896 55.418 1710 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.42 % Allowed : 17.87 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1192 helix: 1.62 (0.33), residues: 254 sheet: 1.99 (0.25), residues: 382 loop : 0.17 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.002 0.000 HIS M 34 PHE 0.014 0.001 PHE D 62 TYR 0.045 0.002 TYR C 94 ARG 0.002 0.000 ARG L 211 *********************** 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 234 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8437 (OUTLIER) cc_final: 0.6788 (p90) REVERT: C 94 TYR cc_start: 0.9320 (m-80) cc_final: 0.9109 (m-80) REVERT: C 116 LYS cc_start: 0.8608 (mttt) cc_final: 0.8405 (mmmt) REVERT: C 137 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8069 (m-30) REVERT: C 197 MET cc_start: 0.9635 (ttm) cc_final: 0.9386 (ttp) REVERT: D 116 LYS cc_start: 0.8472 (mttt) cc_final: 0.7984 (mttt) REVERT: H 5 GLN cc_start: 0.8548 (tt0) cc_final: 0.8162 (tp40) REVERT: H 64 LYS cc_start: 0.9017 (tttt) cc_final: 0.8549 (ttpp) REVERT: H 72 ASP cc_start: 0.8150 (t0) cc_final: 0.7529 (t0) REVERT: H 77 THR cc_start: 0.8989 (m) cc_final: 0.8454 (p) REVERT: H 85 GLU cc_start: 0.9085 (tp30) cc_final: 0.8860 (tp30) REVERT: H 86 ASP cc_start: 0.8360 (m-30) cc_final: 0.7878 (m-30) REVERT: H 154 TRP cc_start: 0.8271 (m100) cc_final: 0.7934 (m100) REVERT: H 161 SER cc_start: 0.8125 (m) cc_final: 0.7868 (p) REVERT: H 195 ILE cc_start: 0.6291 (OUTLIER) cc_final: 0.6004 (mm) REVERT: I 64 LYS cc_start: 0.8945 (tttt) cc_final: 0.8520 (ttpp) REVERT: I 72 ASP cc_start: 0.8178 (t0) cc_final: 0.7561 (t0) REVERT: I 77 THR cc_start: 0.9007 (m) cc_final: 0.8465 (p) REVERT: I 154 TRP cc_start: 0.8281 (m100) cc_final: 0.7906 (m100) REVERT: I 161 SER cc_start: 0.8196 (m) cc_final: 0.7893 (p) REVERT: I 195 ILE cc_start: 0.6421 (OUTLIER) cc_final: 0.6110 (mm) REVERT: I 214 LYS cc_start: 0.8443 (mttt) cc_final: 0.7899 (tptt) REVERT: L 79 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7327 (mt-10) REVERT: L 82 ASP cc_start: 0.8794 (m-30) cc_final: 0.8440 (m-30) REVERT: L 118 PHE cc_start: 0.8539 (m-80) cc_final: 0.8047 (m-80) REVERT: L 124 GLN cc_start: 0.7773 (tt0) cc_final: 0.7102 (tt0) REVERT: M 24 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8028 (ttp80) REVERT: M 79 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7312 (mt-10) REVERT: M 82 ASP cc_start: 0.8777 (m-30) cc_final: 0.8367 (m-30) REVERT: M 118 PHE cc_start: 0.8505 (m-80) cc_final: 0.7964 (m-80) REVERT: M 124 GLN cc_start: 0.7346 (tt0) cc_final: 0.6710 (tt0) REVERT: M 126 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7716 (tppt) outliers start: 35 outliers final: 22 residues processed: 225 average time/residue: 0.1915 time to fit residues: 61.6744 Evaluate side-chains 218 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain 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 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.157429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106726 restraints weight = 16052.090| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.45 r_work: 0.3179 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9582 Z= 0.257 Angle : 0.617 11.195 13058 Z= 0.305 Chirality : 0.042 0.155 1490 Planarity : 0.005 0.045 1608 Dihedral : 6.951 55.110 1710 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.83 % Allowed : 19.43 % Favored : 77.73 % 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: 1.67 (0.25), residues: 1192 helix: 1.83 (0.34), residues: 238 sheet: 1.94 (0.25), residues: 382 loop : 0.25 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 89 HIS 0.003 0.001 HIS D 63 PHE 0.022 0.002 PHE D 62 TYR 0.042 0.002 TYR C 94 ARG 0.001 0.000 ARG D 109 *********************** 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 220 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8483 (OUTLIER) cc_final: 0.6810 (p90) REVERT: C 116 LYS cc_start: 0.8637 (mttt) cc_final: 0.8433 (mmmt) REVERT: C 137 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: D 116 LYS cc_start: 0.8475 (mttt) cc_final: 0.7976 (mttt) REVERT: H 5 GLN cc_start: 0.8576 (tt0) cc_final: 0.8158 (tp40) REVERT: H 64 LYS cc_start: 0.9047 (tttt) cc_final: 0.8587 (ttpp) REVERT: H 72 ASP cc_start: 0.8182 (t0) cc_final: 0.7582 (t0) REVERT: H 77 THR cc_start: 0.8989 (m) cc_final: 0.8409 (p) REVERT: H 85 GLU cc_start: 0.9076 (tp30) cc_final: 0.8858 (tp30) REVERT: H 86 ASP cc_start: 0.8354 (m-30) cc_final: 0.7900 (m-30) REVERT: H 154 TRP cc_start: 0.8267 (m100) cc_final: 0.7929 (m100) REVERT: H 161 SER cc_start: 0.8235 (m) cc_final: 0.7915 (p) REVERT: H 195 ILE cc_start: 0.6280 (OUTLIER) cc_final: 0.5988 (mm) REVERT: I 64 LYS cc_start: 0.8980 (tttt) cc_final: 0.8561 (ttpp) REVERT: I 72 ASP cc_start: 0.8237 (t0) cc_final: 0.7638 (t0) REVERT: I 77 THR cc_start: 0.9006 (m) cc_final: 0.8384 (p) REVERT: I 154 TRP cc_start: 0.8277 (m100) cc_final: 0.7885 (m100) REVERT: I 161 SER cc_start: 0.8237 (m) cc_final: 0.7948 (p) REVERT: I 195 ILE cc_start: 0.6392 (OUTLIER) cc_final: 0.6089 (mm) REVERT: I 214 LYS cc_start: 0.8437 (mttt) cc_final: 0.7945 (tptt) REVERT: L 79 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7408 (mt-10) REVERT: L 82 ASP cc_start: 0.8778 (m-30) cc_final: 0.8375 (m-30) REVERT: L 118 PHE cc_start: 0.8575 (m-80) cc_final: 0.7947 (m-80) REVERT: L 124 GLN cc_start: 0.7740 (tt0) cc_final: 0.7083 (tt0) REVERT: L 211 ARG cc_start: 0.7768 (ptm-80) cc_final: 0.7534 (ptm-80) REVERT: M 24 ARG cc_start: 0.8392 (ttm110) cc_final: 0.8035 (ttp80) REVERT: M 79 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7367 (mt-10) REVERT: M 82 ASP cc_start: 0.8752 (m-30) cc_final: 0.8343 (m-30) REVERT: M 118 PHE cc_start: 0.8545 (m-80) cc_final: 0.7958 (m-80) REVERT: M 124 GLN cc_start: 0.7285 (tt0) cc_final: 0.6671 (tt0) REVERT: M 126 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7683 (tppt) outliers start: 29 outliers final: 23 residues processed: 212 average time/residue: 0.1826 time to fit residues: 55.7036 Evaluate side-chains 215 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 19 optimal weight: 0.0060 chunk 7 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104942 restraints weight = 16273.417| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.45 r_work: 0.3160 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9582 Z= 0.295 Angle : 0.642 11.021 13058 Z= 0.319 Chirality : 0.043 0.156 1490 Planarity : 0.005 0.045 1608 Dihedral : 7.057 54.816 1710 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.83 % Allowed : 18.85 % 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: 1.54 (0.24), residues: 1192 helix: 1.74 (0.34), residues: 238 sheet: 1.86 (0.25), residues: 382 loop : 0.17 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 89 HIS 0.003 0.001 HIS M 34 PHE 0.023 0.002 PHE D 62 TYR 0.057 0.002 TYR C 94 ARG 0.002 0.000 ARG H 94 ********************** 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 215 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8501 (OUTLIER) cc_final: 0.6736 (p90) REVERT: C 137 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: D 116 LYS cc_start: 0.8411 (mttt) cc_final: 0.7936 (mttt) REVERT: H 5 GLN cc_start: 0.8574 (tt0) cc_final: 0.8126 (tp40) REVERT: H 64 LYS cc_start: 0.9076 (tttt) cc_final: 0.8631 (ttpp) REVERT: H 72 ASP cc_start: 0.8214 (t0) cc_final: 0.7607 (t0) REVERT: H 77 THR cc_start: 0.8977 (m) cc_final: 0.8322 (p) REVERT: H 85 GLU cc_start: 0.9089 (tp30) cc_final: 0.8866 (tp30) REVERT: H 86 ASP cc_start: 0.8393 (m-30) cc_final: 0.7899 (m-30) REVERT: H 154 TRP cc_start: 0.8289 (m100) cc_final: 0.7938 (m100) REVERT: H 161 SER cc_start: 0.8243 (m) cc_final: 0.7933 (p) REVERT: H 195 ILE cc_start: 0.6477 (OUTLIER) cc_final: 0.6199 (mm) REVERT: I 64 LYS cc_start: 0.9022 (tttt) cc_final: 0.8563 (ttpp) REVERT: I 72 ASP cc_start: 0.8251 (t0) cc_final: 0.7641 (t0) REVERT: I 77 THR cc_start: 0.9008 (m) cc_final: 0.8327 (p) REVERT: I 154 TRP cc_start: 0.8298 (m100) cc_final: 0.7886 (m100) REVERT: I 161 SER cc_start: 0.8388 (m) cc_final: 0.8096 (p) REVERT: I 195 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.6082 (mm) REVERT: I 214 LYS cc_start: 0.8398 (mttt) cc_final: 0.7879 (tptt) REVERT: L 79 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7455 (mt-10) REVERT: L 82 ASP cc_start: 0.8849 (m-30) cc_final: 0.8411 (m-30) REVERT: L 118 PHE cc_start: 0.8607 (m-80) cc_final: 0.7941 (m-80) REVERT: L 124 GLN cc_start: 0.7765 (tt0) cc_final: 0.7063 (tt0) REVERT: M 24 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8046 (ttp80) REVERT: M 79 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7333 (mt-10) REVERT: M 82 ASP cc_start: 0.8801 (m-30) cc_final: 0.8393 (m-30) REVERT: M 118 PHE cc_start: 0.8545 (m-80) cc_final: 0.7981 (m-80) REVERT: M 124 GLN cc_start: 0.7399 (tt0) cc_final: 0.7157 (tt0) REVERT: M 126 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7661 (tppt) REVERT: M 167 ASP cc_start: 0.7448 (t70) cc_final: 0.6983 (t70) outliers start: 29 outliers final: 22 residues processed: 207 average time/residue: 0.1971 time to fit residues: 58.6784 Evaluate side-chains 209 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 196 CYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 71 optimal weight: 10.0000 chunk 54 optimal weight: 0.0670 chunk 52 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 77 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.157692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.107651 restraints weight = 15886.858| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.46 r_work: 0.3191 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9582 Z= 0.208 Angle : 0.606 10.870 13058 Z= 0.298 Chirality : 0.042 0.152 1490 Planarity : 0.004 0.044 1608 Dihedral : 6.906 56.078 1710 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.83 % Allowed : 19.24 % Favored : 77.93 % 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: 1.65 (0.25), residues: 1192 helix: 1.91 (0.34), residues: 238 sheet: 1.92 (0.25), residues: 382 loop : 0.21 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 89 HIS 0.002 0.000 HIS M 34 PHE 0.017 0.001 PHE D 62 TYR 0.040 0.002 TYR C 94 ARG 0.001 0.000 ARG D 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4700.40 seconds wall clock time: 84 minutes 31.89 seconds (5071.89 seconds total)