Starting phenix.real_space_refine on Sat May 10 15:25:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zab_39877/05_2025/8zab_39877.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zab_39877/05_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_39877/05_2025/8zab_39877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zab_39877/05_2025/8zab_39877.map" model { file = "/net/cci-nas-00/data/ceres_data/8zab_39877/05_2025/8zab_39877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zab_39877/05_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-5687/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: 5.68, 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: 1.49 Conformation dependent library (CDL) restraints added in 973.8 milliseconds 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: 1.04 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: 1.87 Time building geometry restraints manager: 1.80 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: 2.690 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.500 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- 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 : 0.681 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: 0.1994 time to fit residues: 33.7188 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 : 0.716 ------------------------------------------------------------------------------- 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 = 17539.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.101955 restraints weight = 12860.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103205 restraints weight = 11767.910| |-----------------------------------------------------------------------------| 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 40.804 920 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 7.66656 ( 495) SS BOND : bond 0.00716 ( 8) SS BOND : angle 1.12432 ( 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 : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.5530 (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: 0.7150 (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: 0.8140 (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: 0.6779 (tpp) outliers start: 53 outliers final: 27 residues processed: 137 average time/residue: 0.1641 time to fit residues: 30.2709 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 : 0.681 ------------------------------------------------------------------------------- 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: 1.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.0370 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.119468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102764 restraints weight = 17683.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.102399 restraints weight = 12822.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.103422 restraints weight = 12707.292| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6641 Z= 0.171 Angle : 0.654 13.047 9003 Z= 0.337 Chirality : 0.047 0.219 998 Planarity : 0.007 0.143 1167 Dihedral : 5.159 41.050 920 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.02 % Favored : 94.74 % Rotamer: Outliers : 5.56 % Allowed : 27.49 % Favored : 66.95 % 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: -0.22 (0.28), residues: 378 loop : -1.32 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 38 HIS 0.003 0.001 HIS D 24 PHE 0.016 0.002 PHE E 39 TYR 0.023 0.001 TYR G 98 ARG 0.004 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 186) hydrogen bonds : angle 6.90416 ( 495) SS BOND : bond 0.00525 ( 8) SS BOND : angle 0.89568 ( 16) covalent geometry : bond 0.00391 ( 6633) covalent geometry : angle 0.65391 ( 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 130 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: C 17 GLU cc_start: 0.7160 (pm20) cc_final: 0.6890 (pp20) REVERT: C 136 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6489 (mm-30) REVERT: E 204 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8138 (m) REVERT: G 105 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.5089 (p90) REVERT: G 129 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7814 (mm-30) REVERT: G 183 ASP cc_start: 0.8106 (t0) cc_final: 0.7817 (t0) outliers start: 39 outliers final: 28 residues processed: 122 average time/residue: 0.1575 time to fit residues: 26.4574 Evaluate side-chains 111 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 96 LEU 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 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 114 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 158 ILE 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 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 82 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 46 optimal weight: 0.0470 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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** 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 = 0.3963 r_free = 0.3963 target = 0.119831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.102935 restraints weight = 17668.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.102861 restraints weight = 12493.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.103705 restraints weight = 13058.732| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6641 Z= 0.155 Angle : 0.628 12.062 9003 Z= 0.325 Chirality : 0.047 0.221 998 Planarity : 0.006 0.138 1167 Dihedral : 5.036 40.849 920 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.50 % Favored : 94.26 % Rotamer: Outliers : 7.41 % Allowed : 26.21 % 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: -1.19 (0.29), residues: 836 helix: None (None), residues: 0 sheet: -0.26 (0.28), residues: 376 loop : -1.24 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 150 HIS 0.003 0.001 HIS D 24 PHE 0.024 0.002 PHE E 212 TYR 0.021 0.001 TYR G 98 ARG 0.003 0.000 ARG E 54 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 186) hydrogen bonds : angle 6.59341 ( 495) SS BOND : bond 0.00429 ( 8) SS BOND : angle 0.79829 ( 16) covalent geometry : bond 0.00358 ( 6633) covalent geometry : angle 0.62736 ( 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 136 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 84 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: C 128 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6984 (m-80) REVERT: C 136 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6389 (mm-30) REVERT: C 213 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.5894 (t80) REVERT: D 158 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.7021 (mp) REVERT: E 204 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8193 (m) REVERT: G 105 TYR cc_start: 0.5511 (OUTLIER) cc_final: 0.5222 (p90) REVERT: G 129 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7776 (mm-30) REVERT: G 183 ASP cc_start: 0.7904 (t0) cc_final: 0.7672 (t0) outliers start: 52 outliers final: 33 residues processed: 131 average time/residue: 0.1755 time to fit residues: 30.8501 Evaluate side-chains 116 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 148 ILE 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 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 68 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 123 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 74 ASP Chi-restraints excluded: chain G residue 82 LEU 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 164 VAL Chi-restraints excluded: chain G residue 179 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: 3.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** C 153 ASN ** 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 = 0.3952 r_free = 0.3952 target = 0.119181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.102361 restraints weight = 17529.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102125 restraints weight = 12557.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.103238 restraints weight = 12606.492| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6641 Z= 0.172 Angle : 0.647 11.248 9003 Z= 0.330 Chirality : 0.047 0.223 998 Planarity : 0.006 0.134 1167 Dihedral : 5.059 40.295 920 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.10 % Favored : 93.66 % Rotamer: Outliers : 6.84 % Allowed : 27.21 % 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: -1.17 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.30 (0.28), residues: 375 loop : -1.16 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 38 HIS 0.003 0.001 HIS D 24 PHE 0.014 0.002 PHE E 39 TYR 0.023 0.002 TYR G 98 ARG 0.005 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 186) hydrogen bonds : angle 6.58931 ( 495) SS BOND : bond 0.00362 ( 8) SS BOND : angle 0.87079 ( 16) covalent geometry : bond 0.00397 ( 6633) covalent geometry : angle 0.64606 ( 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 128 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 80 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: C 136 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6427 (mm-30) REVERT: C 213 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.5898 (t80) REVERT: D 158 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.7127 (mp) REVERT: E 204 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8239 (m) REVERT: G 105 TYR cc_start: 0.5852 (OUTLIER) cc_final: 0.5595 (p90) REVERT: G 129 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7812 (mm-30) REVERT: G 183 ASP cc_start: 0.7931 (t0) cc_final: 0.7678 (t0) outliers start: 48 outliers final: 35 residues processed: 121 average time/residue: 0.1688 time to fit residues: 28.0654 Evaluate side-chains 117 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 68 THR 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 136 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 148 ILE 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 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 36 VAL Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 179 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 0.0070 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 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 = 0.3975 r_free = 0.3975 target = 0.120806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.103768 restraints weight = 17279.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103505 restraints weight = 12726.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104694 restraints weight = 12574.522| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3228 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= 0.126 Angle : 0.599 11.151 9003 Z= 0.309 Chirality : 0.046 0.221 998 Planarity : 0.006 0.132 1167 Dihedral : 4.821 39.742 920 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.38 % Favored : 94.38 % Rotamer: Outliers : 4.70 % Allowed : 28.92 % 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: -0.99 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.21 (0.27), residues: 390 loop : -1.03 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 38 HIS 0.003 0.001 HIS D 24 PHE 0.014 0.002 PHE E 39 TYR 0.021 0.001 TYR G 98 ARG 0.004 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 186) hydrogen bonds : angle 6.27255 ( 495) SS BOND : bond 0.00354 ( 8) SS BOND : angle 0.86935 ( 16) covalent geometry : bond 0.00289 ( 6633) covalent geometry : angle 0.59851 ( 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 116 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: D 158 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.7002 (mp) REVERT: E 168 ASP cc_start: 0.7276 (p0) cc_final: 0.6357 (p0) REVERT: E 204 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8246 (m) REVERT: G 129 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7900 (mm-30) REVERT: G 183 ASP cc_start: 0.7904 (t0) cc_final: 0.7633 (t0) outliers start: 33 outliers final: 29 residues processed: 112 average time/residue: 0.1595 time to fit residues: 24.4428 Evaluate side-chains 109 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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 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 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 198 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 198 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.0570 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 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 = 0.120804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.103938 restraints weight = 17381.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103577 restraints weight = 12587.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104565 restraints weight = 12701.588| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6641 Z= 0.130 Angle : 0.604 10.764 9003 Z= 0.308 Chirality : 0.046 0.220 998 Planarity : 0.006 0.130 1167 Dihedral : 4.783 39.791 920 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.26 % Favored : 94.50 % Rotamer: Outliers : 5.84 % Allowed : 28.77 % 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: -0.90 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.11 (0.27), residues: 389 loop : -1.00 (0.30), residues: 447 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 0.015 0.002 PHE E 207 TYR 0.021 0.001 TYR G 98 ARG 0.003 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02675 ( 186) hydrogen bonds : angle 6.19022 ( 495) SS BOND : bond 0.00319 ( 8) SS BOND : angle 0.84885 ( 16) covalent geometry : bond 0.00299 ( 6633) covalent geometry : angle 0.60316 ( 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: 41 poor density : 79 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: C 58 ASP cc_start: 0.2259 (OUTLIER) cc_final: 0.1193 (p0) REVERT: D 158 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6953 (mp) REVERT: E 168 ASP cc_start: 0.7025 (p0) cc_final: 0.6452 (p0) REVERT: E 204 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8245 (m) REVERT: G 37 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.5850 (ttm170) REVERT: G 129 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7888 (mm-30) REVERT: G 183 ASP cc_start: 0.7900 (t0) cc_final: 0.7650 (t0) outliers start: 41 outliers final: 34 residues processed: 116 average time/residue: 0.1718 time to fit residues: 26.6219 Evaluate side-chains 112 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 58 ASP 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 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 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 179 VAL 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 37 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 208 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 15 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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** C 48 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.121527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.104642 restraints weight = 17260.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104770 restraints weight = 11455.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.106506 restraints weight = 10866.249| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6641 Z= 0.117 Angle : 0.594 10.647 9003 Z= 0.305 Chirality : 0.046 0.220 998 Planarity : 0.006 0.128 1167 Dihedral : 4.709 39.772 920 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.14 % Favored : 94.62 % Rotamer: Outliers : 5.56 % Allowed : 28.49 % 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: -0.81 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.05 (0.28), residues: 387 loop : -0.94 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 150 HIS 0.002 0.001 HIS D 24 PHE 0.015 0.001 PHE E 207 TYR 0.019 0.001 TYR G 98 ARG 0.003 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02537 ( 186) hydrogen bonds : angle 6.05428 ( 495) SS BOND : bond 0.00333 ( 8) SS BOND : angle 0.77959 ( 16) covalent geometry : bond 0.00270 ( 6633) covalent geometry : angle 0.59362 ( 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 121 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: C 54 LYS cc_start: 0.6380 (OUTLIER) cc_final: 0.6061 (pttm) REVERT: C 58 ASP cc_start: 0.2396 (OUTLIER) cc_final: 0.1362 (p0) REVERT: D 158 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6849 (mp) REVERT: E 168 ASP cc_start: 0.6782 (p0) cc_final: 0.6288 (p0) REVERT: E 204 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.8227 (m) REVERT: G 37 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.5810 (ttm170) REVERT: G 129 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7836 (mm-30) outliers start: 39 outliers final: 31 residues processed: 118 average time/residue: 0.1775 time to fit residues: 28.1668 Evaluate side-chains 116 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 58 ASP 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 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 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 179 VAL 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 37 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 CYS Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 198 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: 0.8980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.119493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.102560 restraints weight = 17639.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102232 restraints weight = 12515.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.103542 restraints weight = 11285.680| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6641 Z= 0.171 Angle : 0.667 9.779 9003 Z= 0.341 Chirality : 0.046 0.219 998 Planarity : 0.006 0.122 1167 Dihedral : 4.947 41.070 920 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.74 % Favored : 94.02 % Rotamer: Outliers : 5.56 % Allowed : 29.34 % Favored : 65.10 % 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: -0.92 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.07 (0.28), residues: 370 loop : -1.05 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 142 HIS 0.003 0.001 HIS D 24 PHE 0.016 0.002 PHE E 207 TYR 0.024 0.002 TYR G 98 ARG 0.002 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02787 ( 186) hydrogen bonds : angle 6.35076 ( 495) SS BOND : bond 0.00386 ( 8) SS BOND : angle 0.88893 ( 16) covalent geometry : bond 0.00397 ( 6633) covalent geometry : angle 0.66669 ( 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: 39 poor density : 76 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: C 58 ASP cc_start: 0.2512 (OUTLIER) cc_final: 0.1477 (p0) REVERT: C 136 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6539 (mm-30) REVERT: D 158 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6991 (mp) REVERT: E 168 ASP cc_start: 0.6931 (p0) cc_final: 0.6386 (p0) REVERT: E 204 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8240 (m) REVERT: G 129 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7742 (mm-30) outliers start: 39 outliers final: 35 residues processed: 109 average time/residue: 0.1730 time to fit residues: 25.7277 Evaluate side-chains 115 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 76 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 58 ASP 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 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 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 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 Chi-restraints excluded: chain G residue 198 LEU 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 34 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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** ** 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 = 0.3943 r_free = 0.3943 target = 0.118852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.101959 restraints weight = 17577.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101609 restraints weight = 12627.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.102933 restraints weight = 11414.821| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3571 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= 0.187 Angle : 0.670 8.889 9003 Z= 0.343 Chirality : 0.047 0.218 998 Planarity : 0.006 0.121 1167 Dihedral : 5.080 41.794 920 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.34 % Favored : 93.42 % Rotamer: Outliers : 5.70 % Allowed : 29.20 % Favored : 65.10 % 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: -1.05 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.17 (0.28), residues: 370 loop : -1.12 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 38 HIS 0.003 0.001 HIS D 134 PHE 0.016 0.002 PHE G 99 TYR 0.024 0.002 TYR G 98 ARG 0.002 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02881 ( 186) hydrogen bonds : angle 6.50483 ( 495) SS BOND : bond 0.00410 ( 8) SS BOND : angle 0.93266 ( 16) covalent geometry : bond 0.00434 ( 6633) covalent geometry : angle 0.66981 ( 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 114 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 74 time to evaluate : 0.762 Fit side-chains REVERT: C 58 ASP cc_start: 0.2451 (OUTLIER) cc_final: 0.1334 (p0) REVERT: C 136 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6505 (mm-30) REVERT: D 158 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.7060 (mp) REVERT: E 168 ASP cc_start: 0.6932 (p0) cc_final: 0.6299 (p0) REVERT: E 204 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8276 (m) REVERT: G 129 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7781 (mm-30) outliers start: 40 outliers final: 35 residues processed: 109 average time/residue: 0.1623 time to fit residues: 24.2719 Evaluate side-chains 113 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 58 ASP Chi-restraints excluded: chain C residue 68 THR 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 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 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 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 Chi-restraints excluded: chain G residue 198 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** 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 = 0.3954 r_free = 0.3954 target = 0.119817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.103214 restraints weight = 17831.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.103009 restraints weight = 12913.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.104220 restraints weight = 11669.915| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6641 Z= 0.167 Angle : 0.668 9.514 9003 Z= 0.342 Chirality : 0.046 0.216 998 Planarity : 0.006 0.120 1167 Dihedral : 5.032 41.644 920 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.10 % Favored : 93.66 % Rotamer: Outliers : 5.84 % Allowed : 29.34 % 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: -1.05 (0.30), residues: 836 helix: None (None), residues: 0 sheet: -0.18 (0.28), residues: 370 loop : -1.11 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 38 HIS 0.002 0.001 HIS D 24 PHE 0.015 0.002 PHE E 39 TYR 0.023 0.002 TYR G 98 ARG 0.003 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 186) hydrogen bonds : angle 6.47406 ( 495) SS BOND : bond 0.00371 ( 8) SS BOND : angle 0.87243 ( 16) covalent geometry : bond 0.00390 ( 6633) covalent geometry : angle 0.66752 ( 8987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.19 seconds wall clock time: 41 minutes 27.95 seconds (2487.95 seconds total)