Starting phenix.real_space_refine on Thu Jun 5 16:55:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zab_39877/06_2025/8zab_39877.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zab_39877/06_2025/8zab_39877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zab_39877/06_2025/8zab_39877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zab_39877/06_2025/8zab_39877.map" model { file = "/net/cci-nas-00/data/ceres_data/8zab_39877/06_2025/8zab_39877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zab_39877/06_2025/8zab_39877.cif" } resolution = 3.67 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= 0.001 sd= 0.041 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 38 5.16 5 C 4098 2.51 5 N 1127 2.21 5 O 1234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6497 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1576 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 8, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1600 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1685 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1636 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 197} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 5.63, per 1000 atoms: 0.87 Number of scatterers: 6497 At special positions: 0 Unit cell: (86.184, 151.899, 93.7251, 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 38 16.00 O 1234 8.00 N 1127 7.00 C 4098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 191 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.04 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 191 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 191 " 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: 1.68 Conformation dependent library (CDL) restraints added in 1.0 seconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 18 sheets defined 6.5% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'C' and resid 57 through 60 removed outlier: 3.522A pdb=" N GLN C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 71 through 78 removed outlier: 4.383A pdb=" N GLY C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA C 77 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 213 Processing helix chain 'D' and resid 210 through 213 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.537A pdb=" N ARG E 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 209 through 213 removed outlier: 3.774A pdb=" N MET E 213 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 61 through 65 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 209 through 213 removed outlier: 3.507A pdb=" N PHE G 212 " --> pdb=" O PRO G 209 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET G 213 " --> pdb=" O GLU G 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 209 through 213' Processing sheet with id=AA1, first strand: chain 'C' and resid 11 through 14 removed outlier: 5.833A pdb=" N ILE C 11 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA C 115 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 13 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 36 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.667A pdb=" N ALA C 177 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 179 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C 181 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 133 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR C 140 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 175 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.667A pdb=" N ALA C 177 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 179 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C 181 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 133 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR C 128 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS C 134 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL C 123 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 147 through 151 removed outlier: 3.692A pdb=" N LEU C 200 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL D 123 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER C 205 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL D 125 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER C 207 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY D 127 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS D 134 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR D 173 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 151 removed outlier: 3.692A pdb=" N LEU C 200 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL D 123 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER C 205 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL D 125 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER C 207 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY D 127 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS D 134 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR D 173 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 166 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.685A pdb=" N ALA D 81 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.093A pdb=" N ILE D 11 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA D 115 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA D 13 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU D 36 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL D 49 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP D 38 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 147 through 151 removed outlier: 3.667A pdb=" N THR D 192 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 193 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.719A pdb=" N SER E 104 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY E 93 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL E 49 " --> pdb=" O ARG E 56 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS E 51 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG E 54 " --> pdb=" O LYS E 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 122 through 128 removed outlier: 3.515A pdb=" N LEU E 122 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG E 134 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ARG E 134 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE E 181 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLU E 136 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL E 179 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE E 138 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR E 177 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG E 140 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL E 175 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET E 174 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS E 162 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.531A pdb=" N LYS E 202 " --> pdb=" O ILE E 193 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN E 200 " --> pdb=" O ASN E 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.295A pdb=" N ILE G 11 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ALA G 115 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA G 13 " --> pdb=" O ALA G 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.668A pdb=" N LEU G 21 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU G 82 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS G 23 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 80 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA G 81 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 48 through 52 removed outlier: 3.504A pdb=" N PHE G 48 " --> pdb=" O TRP G 38 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET G 34 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU G 35 " --> pdb=" O GLN G 100 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN G 100 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 122 through 129 removed outlier: 5.816A pdb=" N ILE G 123 " --> pdb=" O ILE G 138 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE G 138 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET G 125 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU G 136 " --> pdb=" O MET G 125 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY G 127 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS G 162 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 147 through 151 213 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2159 1.34 - 1.46: 1484 1.46 - 1.58: 2928 1.58 - 1.70: 2 1.70 - 1.82: 60 Bond restraints: 6633 Sorted by residual: bond pdb=" CB PRO C 10 " pdb=" CG PRO C 10 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.93e+00 bond pdb=" CB PRO D 159 " pdb=" CG PRO D 159 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.63e+00 bond pdb=" CB PRO C 159 " pdb=" CG PRO C 159 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.02e+00 bond pdb=" CB ASP G 130 " pdb=" CG ASP G 130 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.84e+00 bond pdb=" CB ARG G 103 " pdb=" CG ARG G 103 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.36e+00 ... (remaining 6628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 8899 3.12 - 6.23: 75 6.23 - 9.35: 9 9.35 - 12.46: 2 12.46 - 15.58: 2 Bond angle restraints: 8987 Sorted by residual: angle pdb=" CA PRO C 10 " pdb=" N PRO C 10 " pdb=" CD PRO C 10 " ideal model delta sigma weight residual 112.00 99.21 12.79 1.40e+00 5.10e-01 8.35e+01 angle pdb=" CA PRO D 159 " pdb=" N PRO D 159 " pdb=" CD PRO D 159 " ideal model delta sigma weight residual 112.00 99.62 12.38 1.40e+00 5.10e-01 7.82e+01 angle pdb=" C LEU D 43 " pdb=" N ARG D 44 " pdb=" CA ARG D 44 " ideal model delta sigma weight residual 121.70 137.28 -15.58 1.80e+00 3.09e-01 7.49e+01 angle pdb=" C LEU C 43 " pdb=" N ARG C 44 " pdb=" CA ARG C 44 " ideal model delta sigma weight residual 121.70 132.89 -11.19 1.80e+00 3.09e-01 3.86e+01 angle pdb=" N PRO C 10 " pdb=" CD PRO C 10 " pdb=" CG PRO C 10 " ideal model delta sigma weight residual 103.20 95.00 8.20 1.50e+00 4.44e-01 2.99e+01 ... (remaining 8982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 3368 16.95 - 33.91: 477 33.91 - 50.86: 132 50.86 - 67.81: 26 67.81 - 84.76: 2 Dihedral angle restraints: 4005 sinusoidal: 1597 harmonic: 2408 Sorted by residual: dihedral pdb=" CA PHE D 26 " pdb=" C PHE D 26 " pdb=" N PRO D 27 " pdb=" CA PRO D 27 " ideal model delta harmonic sigma weight residual 180.00 134.92 45.08 0 5.00e+00 4.00e-02 8.13e+01 dihedral pdb=" CB CYS D 137 " pdb=" SG CYS D 137 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -131.08 45.08 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS E 137 " pdb=" SG CYS E 137 " pdb=" SG CYS E 191 " pdb=" CB CYS E 191 " ideal model delta sinusoidal sigma weight residual -86.00 -125.87 39.87 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 4002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 671 0.039 - 0.078: 214 0.078 - 0.118: 104 0.118 - 0.157: 8 0.157 - 0.196: 1 Chirality restraints: 998 Sorted by residual: chirality pdb=" CA PRO D 159 " pdb=" N PRO D 159 " pdb=" C PRO D 159 " pdb=" CB PRO D 159 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA PRO C 10 " pdb=" N PRO C 10 " pdb=" C PRO C 10 " pdb=" CB PRO C 10 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE E 3 " pdb=" N ILE E 3 " pdb=" C ILE E 3 " pdb=" CB ILE E 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 995 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 158 " -0.090 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO D 159 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO D 159 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 159 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 9 " 0.078 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO C 10 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO C 10 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 10 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 158 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO C 159 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO C 159 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 159 " -0.056 5.00e-02 4.00e+02 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 377 2.72 - 3.27: 6265 3.27 - 3.81: 10125 3.81 - 4.36: 11817 4.36 - 4.90: 20603 Nonbonded interactions: 49187 Sorted by model distance: nonbonded pdb=" OD1 ASP G 183 " pdb=" N LYS G 184 " model vdw 2.176 3.120 nonbonded pdb=" N GLN C 100 " pdb=" OE1 GLN C 100 " model vdw 2.201 3.120 nonbonded pdb=" NH1 ARG E 67 " pdb=" OE2 GLU E 91 " model vdw 2.225 3.120 nonbonded pdb=" O VAL D 46 " pdb=" OG SER D 61 " model vdw 2.240 3.040 nonbonded pdb=" N GLU E 58 " pdb=" OE1 GLU E 58 " model vdw 2.248 3.120 ... (remaining 49182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 127 or (resid 128 and (name N or name CA or name \ C or name O or name CB )) or resid 129 through 213)) selection = (chain 'D' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 183 or resid 188 through 202 or \ (resid 203 through 204 and (name N or name CA or name C or name O or name CB )) \ or resid 205 through 213)) } ncs_group { reference = (chain 'E' and (resid 5 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 103 or (resid 104 and (name N or na \ me CA or name C or name O or name CB )) or resid 105 through 106 or (resid 107 t \ hrough 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 151 or (resid 152 and (name N or name CA or name C or name O or name CB \ )) or resid 153 through 214)) selection = chain 'G' } 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 group one per residue 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: 4.330 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.180 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.005 0.158 6641 Z= 0.173 Angle : 0.796 15.579 9003 Z= 0.444 Chirality : 0.046 0.196 998 Planarity : 0.008 0.127 1167 Dihedral : 16.465 84.762 2443 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.46 % Favored : 93.30 % Rotamer: Outliers : 0.28 % Allowed : 33.90 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -1.13 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.06 (0.29), residues: 366 loop : -1.33 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 150 HIS 0.004 0.001 HIS D 24 PHE 0.014 0.001 PHE E 43 TYR 0.020 0.001 TYR G 98 ARG 0.012 0.001 ARG E 54 Details of bonding type rmsd hydrogen bonds : bond 0.28861 ( 186) hydrogen bonds : angle 11.36225 ( 495) SS BOND : bond 0.00504 ( 8) SS BOND : angle 0.89397 ( 16) covalent geometry : bond 0.00459 ( 6633) covalent geometry : angle 0.79612 ( 8987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 ILE cc_start: 0.8790 (tp) cc_final: 0.8472 (mm) REVERT: E 49 VAL cc_start: 0.9275 (t) cc_final: 0.9034 (m) REVERT: E 168 ASP cc_start: 0.6886 (p0) cc_final: 0.6683 (p0) REVERT: G 129 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7556 (mm-30) outliers start: 2 outliers final: 0 residues processed: 132 average time/residue: 0.2107 time to fit residues: 35.7699 Evaluate side-chains 87 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.119087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.102421 restraints weight = 17539.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.101956 restraints weight = 12860.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103203 restraints weight = 11766.942| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 6641 Z= 0.235 Angle : 0.725 7.809 9003 Z= 0.381 Chirality : 0.049 0.199 998 Planarity : 0.007 0.129 1167 Dihedral : 5.376 40.803 920 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.46 % Favored : 93.30 % Rotamer: Outliers : 7.55 % Allowed : 27.64 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -1.35 (0.29), residues: 836 helix: None (None), residues: 0 sheet: -0.37 (0.27), residues: 386 loop : -1.36 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 38 HIS 0.004 0.001 HIS D 122 PHE 0.020 0.002 PHE G 99 TYR 0.030 0.002 TYR G 98 ARG 0.006 0.001 ARG E 54 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 186) hydrogen bonds : angle 7.66658 ( 495) SS BOND : bond 0.00716 ( 8) SS BOND : angle 1.12431 ( 16) covalent geometry : bond 0.00545 ( 6633) covalent geometry : angle 0.72408 ( 8987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 93 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.5531 (tm-30) cc_final: 0.5304 (tm-30) REVERT: C 128 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: C 136 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6592 (mm-30) REVERT: C 213 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.5695 (t80) REVERT: D 133 ILE cc_start: 0.7414 (mm) cc_final: 0.7177 (mm) REVERT: G 105 TYR cc_start: 0.5260 (OUTLIER) cc_final: 0.4937 (p90) REVERT: G 129 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7795 (mm-30) REVERT: G 183 ASP cc_start: 0.8161 (t0) cc_final: 0.7924 (t0) REVERT: G 213 MET cc_start: 0.7012 (mtp) cc_final: 0.6780 (tpp) outliers start: 53 outliers final: 27 residues processed: 137 average time/residue: 0.1620 time to fit residues: 30.2046 Evaluate side-chains 110 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 128 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.0020 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 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 = 0.3990 r_free = 0.3990 target = 0.121285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.104534 restraints weight = 17696.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104232 restraints weight = 12689.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.105375 restraints weight = 13183.167| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6641 Z= 0.128 Angle : 0.626 12.435 9003 Z= 0.323 Chirality : 0.047 0.216 998 Planarity : 0.007 0.140 1167 Dihedral : 4.991 40.978 920 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.55 % Favored : 95.22 % Rotamer: Outliers : 3.70 % Allowed : 29.06 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -1.11 (0.29), residues: 836 helix: None (None), residues: 0 sheet: -0.21 (0.27), residues: 395 loop : -1.21 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 150 HIS 0.003 0.001 HIS D 24 PHE 0.012 0.001 PHE E 39 TYR 0.020 0.001 TYR G 98 ARG 0.004 0.000 ARG E 54 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 186) hydrogen bonds : angle 6.66001 ( 495) SS BOND : bond 0.00359 ( 8) SS BOND : angle 0.81026 ( 16) covalent geometry : bond 0.00294 ( 6633) covalent geometry : angle 0.62531 ( 8987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: C 17 GLU cc_start: 0.7166 (pm20) cc_final: 0.6862 (pp20) REVERT: C 106 GLU cc_start: 0.5226 (tm-30) cc_final: 0.5012 (tm-30) REVERT: E 204 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.8085 (m) REVERT: G 105 TYR cc_start: 0.5240 (OUTLIER) cc_final: 0.4914 (p90) REVERT: G 129 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7838 (mm-30) REVERT: G 183 ASP cc_start: 0.8060 (t0) cc_final: 0.7774 (t0) outliers start: 26 outliers final: 18 residues processed: 112 average time/residue: 0.1702 time to fit residues: 25.8916 Evaluate side-chains 101 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 HIS ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.120499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.103610 restraints weight = 17651.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103507 restraints weight = 12372.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104637 restraints weight = 11329.632| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6641 Z= 0.148 Angle : 0.617 12.165 9003 Z= 0.319 Chirality : 0.046 0.221 998 Planarity : 0.006 0.138 1167 Dihedral : 4.928 40.590 920 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.50 % Favored : 94.26 % Rotamer: Outliers : 6.55 % Allowed : 26.64 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -1.10 (0.29), residues: 836 helix: None (None), residues: 0 sheet: -0.27 (0.27), residues: 396 loop : -1.13 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 38 HIS 0.003 0.001 HIS D 24 PHE 0.023 0.002 PHE E 212 TYR 0.023 0.001 TYR G 98 ARG 0.003 0.000 ARG E 54 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 186) hydrogen bonds : angle 6.50491 ( 495) SS BOND : bond 0.00374 ( 8) SS BOND : angle 0.87604 ( 16) covalent geometry : bond 0.00341 ( 6633) covalent geometry : angle 0.61637 ( 8987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: C 128 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.7021 (m-80) REVERT: C 136 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6378 (mm-30) REVERT: C 213 PHE cc_start: 0.6579 (OUTLIER) cc_final: 0.5823 (t80) REVERT: D 158 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6889 (mp) REVERT: E 204 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8158 (m) REVERT: G 105 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.5076 (p90) REVERT: G 129 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7821 (mm-30) REVERT: G 183 ASP cc_start: 0.7906 (t0) cc_final: 0.7644 (t0) outliers start: 46 outliers final: 26 residues processed: 126 average time/residue: 0.1779 time to fit residues: 30.2182 Evaluate side-chains 112 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 164 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 77 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 7 optimal weight: 0.0040 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 HIS ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.120615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103689 restraints weight = 17637.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.103355 restraints weight = 12964.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.104460 restraints weight = 13325.760| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6641 Z= 0.160 Angle : 0.628 11.369 9003 Z= 0.322 Chirality : 0.046 0.221 998 Planarity : 0.006 0.134 1167 Dihedral : 4.961 40.147 920 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.02 % Favored : 94.74 % Rotamer: Outliers : 6.27 % Allowed : 27.35 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -1.11 (0.29), residues: 836 helix: None (None), residues: 0 sheet: -0.23 (0.27), residues: 375 loop : -1.16 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 38 HIS 0.003 0.001 HIS D 24 PHE 0.015 0.002 PHE E 39 TYR 0.025 0.001 TYR G 98 ARG 0.003 0.000 ARG E 54 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 186) hydrogen bonds : angle 6.48519 ( 495) SS BOND : bond 0.00377 ( 8) SS BOND : angle 0.86690 ( 16) covalent geometry : bond 0.00368 ( 6633) covalent geometry : angle 0.62790 ( 8987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: C 136 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6421 (mm-30) REVERT: C 213 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.5923 (t80) REVERT: D 158 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7036 (mp) REVERT: E 204 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8208 (m) REVERT: G 105 TYR cc_start: 0.5535 (OUTLIER) cc_final: 0.5279 (p90) REVERT: G 129 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7789 (mm-30) REVERT: G 183 ASP cc_start: 0.7891 (t0) cc_final: 0.7641 (t0) outliers start: 44 outliers final: 30 residues processed: 121 average time/residue: 0.1714 time to fit residues: 28.0707 Evaluate side-chains 114 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 105 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.0170 chunk 9 optimal weight: 0.8980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 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 = 0.3983 r_free = 0.3983 target = 0.121274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.104411 restraints weight = 17230.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.104097 restraints weight = 11883.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.105676 restraints weight = 11534.422| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6641 Z= 0.120 Angle : 0.589 11.175 9003 Z= 0.304 Chirality : 0.046 0.221 998 Planarity : 0.006 0.132 1167 Dihedral : 4.734 39.879 920 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.14 % Favored : 94.62 % Rotamer: Outliers : 5.27 % Allowed : 27.92 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -0.88 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.11 (0.27), residues: 387 loop : -0.97 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 150 HIS 0.003 0.001 HIS D 24 PHE 0.013 0.001 PHE E 39 TYR 0.020 0.001 TYR G 98 ARG 0.006 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02662 ( 186) hydrogen bonds : angle 6.15984 ( 495) SS BOND : bond 0.00336 ( 8) SS BOND : angle 0.80379 ( 16) covalent geometry : bond 0.00276 ( 6633) covalent geometry : angle 0.58884 ( 8987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: C 17 GLU cc_start: 0.6982 (pm20) cc_final: 0.6466 (pp20) REVERT: C 136 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6460 (mm-30) REVERT: D 158 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6900 (mp) REVERT: E 168 ASP cc_start: 0.6852 (p0) cc_final: 0.6231 (p0) REVERT: E 204 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8207 (m) REVERT: G 37 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.5704 (ttm170) REVERT: G 105 TYR cc_start: 0.5587 (OUTLIER) cc_final: 0.5383 (p90) REVERT: G 129 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7847 (mm-30) REVERT: G 183 ASP cc_start: 0.7856 (t0) cc_final: 0.7610 (t0) outliers start: 37 outliers final: 28 residues processed: 117 average time/residue: 0.1918 time to fit residues: 30.3818 Evaluate side-chains 114 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 105 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 2 optimal weight: 0.0020 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 HIS ** 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 = 0.3976 r_free = 0.3976 target = 0.120866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104050 restraints weight = 17323.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103643 restraints weight = 12587.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104821 restraints weight = 12748.507| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6641 Z= 0.134 Angle : 0.602 10.769 9003 Z= 0.307 Chirality : 0.046 0.219 998 Planarity : 0.006 0.130 1167 Dihedral : 4.716 39.636 920 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.38 % Favored : 94.38 % Rotamer: Outliers : 5.56 % Allowed : 27.35 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -0.84 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.09 (0.27), residues: 387 loop : -0.95 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 150 HIS 0.002 0.001 HIS D 24 PHE 0.014 0.001 PHE E 39 TYR 0.022 0.001 TYR G 98 ARG 0.005 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02661 ( 186) hydrogen bonds : angle 6.15573 ( 495) SS BOND : bond 0.00396 ( 8) SS BOND : angle 0.78656 ( 16) covalent geometry : bond 0.00310 ( 6633) covalent geometry : angle 0.60168 ( 8987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: C 136 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6423 (mm-30) REVERT: D 158 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6915 (mp) REVERT: E 168 ASP cc_start: 0.6981 (p0) cc_final: 0.6382 (p0) REVERT: E 204 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8238 (m) REVERT: G 129 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7864 (mm-30) REVERT: G 183 ASP cc_start: 0.7909 (t0) cc_final: 0.7642 (t0) REVERT: G 200 GLN cc_start: 0.7762 (mp10) cc_final: 0.7104 (mp10) outliers start: 39 outliers final: 32 residues processed: 113 average time/residue: 0.1786 time to fit residues: 27.7654 Evaluate side-chains 114 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 66 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 0.0050 chunk 62 optimal weight: 0.0060 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 overall best weight: 0.1706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.123255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.106522 restraints weight = 17165.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106521 restraints weight = 11637.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.107649 restraints weight = 12119.402| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6641 Z= 0.099 Angle : 0.588 10.849 9003 Z= 0.300 Chirality : 0.046 0.217 998 Planarity : 0.006 0.129 1167 Dihedral : 4.557 39.400 920 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.14 % Favored : 94.62 % Rotamer: Outliers : 3.56 % Allowed : 29.91 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -0.67 (0.30), residues: 836 helix: None (None), residues: 0 sheet: 0.05 (0.28), residues: 392 loop : -0.86 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 150 HIS 0.002 0.001 HIS D 24 PHE 0.010 0.001 PHE G 212 TYR 0.015 0.001 TYR G 98 ARG 0.004 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02398 ( 186) hydrogen bonds : angle 5.80558 ( 495) SS BOND : bond 0.00306 ( 8) SS BOND : angle 0.67163 ( 16) covalent geometry : bond 0.00231 ( 6633) covalent geometry : angle 0.58768 ( 8987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5364 (tmtt) REVERT: C 100 GLN cc_start: 0.8043 (pm20) cc_final: 0.7811 (pm20) REVERT: C 192 THR cc_start: 0.8154 (m) cc_final: 0.7838 (p) REVERT: D 158 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6683 (mp) REVERT: E 168 ASP cc_start: 0.6849 (p0) cc_final: 0.6348 (p0) REVERT: E 204 SER cc_start: 0.8425 (OUTLIER) cc_final: 0.8196 (m) REVERT: G 37 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.5769 (ttm170) REVERT: G 129 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7778 (mm-30) outliers start: 25 outliers final: 20 residues processed: 110 average time/residue: 0.2026 time to fit residues: 30.1840 Evaluate side-chains 104 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 208 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.100028 restraints weight = 17823.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.099738 restraints weight = 13140.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.100865 restraints weight = 12287.418| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 6641 Z= 0.308 Angle : 0.753 8.653 9003 Z= 0.388 Chirality : 0.049 0.222 998 Planarity : 0.007 0.122 1167 Dihedral : 5.375 38.548 920 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.30 % Favored : 92.46 % Rotamer: Outliers : 5.70 % Allowed : 28.35 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -1.22 (0.29), residues: 836 helix: None (None), residues: 0 sheet: -0.30 (0.27), residues: 371 loop : -1.24 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 38 HIS 0.004 0.001 HIS D 134 PHE 0.051 0.003 PHE D 26 TYR 0.027 0.003 TYR G 98 ARG 0.004 0.001 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 186) hydrogen bonds : angle 6.91018 ( 495) SS BOND : bond 0.00542 ( 8) SS BOND : angle 1.18234 ( 16) covalent geometry : bond 0.00708 ( 6633) covalent geometry : angle 0.75239 ( 8987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.916 Fit side-chains REVERT: C 54 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.6085 (pttm) REVERT: C 58 ASP cc_start: 0.2359 (OUTLIER) cc_final: 0.1294 (p0) REVERT: C 136 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6730 (mm-30) REVERT: D 158 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7178 (mp) REVERT: E 204 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8290 (m) REVERT: G 129 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7825 (mm-30) outliers start: 40 outliers final: 30 residues processed: 112 average time/residue: 0.1888 time to fit residues: 28.5161 Evaluate side-chains 109 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 HIS ** 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 = 0.3984 r_free = 0.3984 target = 0.121737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104947 restraints weight = 17728.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104681 restraints weight = 12858.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.106274 restraints weight = 11393.257| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6641 Z= 0.122 Angle : 0.642 9.090 9003 Z= 0.330 Chirality : 0.046 0.215 998 Planarity : 0.006 0.121 1167 Dihedral : 4.944 41.590 920 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.62 % Favored : 94.14 % Rotamer: Outliers : 3.28 % Allowed : 31.05 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -0.93 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.08 (0.28), residues: 370 loop : -1.05 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 38 HIS 0.004 0.001 HIS G 24 PHE 0.016 0.001 PHE E 207 TYR 0.018 0.001 TYR G 98 ARG 0.004 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02572 ( 186) hydrogen bonds : angle 6.24177 ( 495) SS BOND : bond 0.00347 ( 8) SS BOND : angle 0.93078 ( 16) covalent geometry : bond 0.00282 ( 6633) covalent geometry : angle 0.64185 ( 8987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.910 Fit side-chains REVERT: C 54 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.6069 (pttm) REVERT: E 204 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8274 (m) REVERT: G 129 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7838 (mm-30) outliers start: 23 outliers final: 19 residues processed: 105 average time/residue: 0.2440 time to fit residues: 34.5985 Evaluate side-chains 99 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 PRO Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 208 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.0000 chunk 6 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.120337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.103511 restraints weight = 17767.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.103631 restraints weight = 11583.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105254 restraints weight = 10942.134| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6641 Z= 0.152 Angle : 0.668 9.305 9003 Z= 0.341 Chirality : 0.046 0.217 998 Planarity : 0.006 0.120 1167 Dihedral : 5.018 41.149 920 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.10 % Favored : 93.66 % Rotamer: Outliers : 3.56 % Allowed : 31.05 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.45 % Cis-general : 0.25 % Twisted Proline : 2.27 % 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: -0.97 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.10 (0.28), residues: 370 loop : -1.09 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 38 HIS 0.002 0.001 HIS D 24 PHE 0.034 0.002 PHE E 212 TYR 0.020 0.001 TYR G 98 ARG 0.004 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02697 ( 186) hydrogen bonds : angle 6.24499 ( 495) SS BOND : bond 0.00469 ( 8) SS BOND : angle 1.17547 ( 16) covalent geometry : bond 0.00354 ( 6633) covalent geometry : angle 0.66720 ( 8987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.80 seconds wall clock time: 52 minutes 7.73 seconds (3127.73 seconds total)