Starting phenix.real_space_refine on Thu Jul 2 18:31:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctu_45919/07_2026/9ctu_45919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctu_45919/07_2026/9ctu_45919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctu_45919/07_2026/9ctu_45919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctu_45919/07_2026/9ctu_45919.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctu_45919/07_2026/9ctu_45919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctu_45919/07_2026/9ctu_45919.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.026 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 2 5.49 5 S 46 5.16 5 C 6212 2.51 5 N 1604 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9714 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 205} Chain: "D" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1606 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Chain: "E" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 205} Chain: "F" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1606 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Chain: "A" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1529 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "B" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1529 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'1PX': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'1PX': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 2.05, per 1000 atoms: 0.21 Number of scatterers: 9714 At special positions: 0 Unit cell: (124.894, 80.289, 131.382, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 46 16.00 P 2 15.00 O 1848 8.00 N 1604 7.00 C 6212 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 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 195 " 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: 0.79 Conformation dependent library (CDL) restraints added in 352.3 milliseconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 20 sheets defined 18.4% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.652A pdb=" N ASP C 86 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'C' and resid 125 through 132 removed outlier: 3.682A pdb=" N GLY C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 4.099A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 191' Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.585A pdb=" N ASP E 86 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 83 through 87' Processing helix chain 'E' and resid 125 through 132 removed outlier: 3.682A pdb=" N GLY E 132 " --> pdb=" O GLN E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 4.099A pdb=" N GLU E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 191' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.895A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 90 Processing helix chain 'A' and resid 18 through 37 Processing helix chain 'A' and resid 43 through 71 removed outlier: 4.281A pdb=" N TRP A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 74 through 107 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.700A pdb=" N PHE A 112 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 37 Processing helix chain 'B' and resid 43 through 71 removed outlier: 4.267A pdb=" N TRP B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 74 through 107 removed outlier: 3.576A pdb=" N ARG B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.775A pdb=" N PHE B 112 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.537A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.104A pdb=" N SER C 135 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 185 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL C 137 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU C 183 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE C 139 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER C 181 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN C 141 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET C 179 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.205A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN C 149 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.455A pdb=" N MET D 34 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.309A pdb=" N TYR D 175 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 170 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR D 176 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA D 168 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER D 178 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS E 111 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E 13 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N MET E 37 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR E 53 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER E 135 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU E 185 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL E 137 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU E 183 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N PHE E 139 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER E 181 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN E 141 " --> pdb=" O MET E 179 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET E 179 " --> pdb=" O ASN E 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.203A pdb=" N TRP E 152 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN E 149 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.676A pdb=" N GLU F 10 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 110 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET F 34 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.307A pdb=" N TYR F 175 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU F 170 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR F 176 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA F 168 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 178 " --> pdb=" O PHE F 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 151 through 154 Processing sheet with id=AB9, first strand: chain 'A' and resid 128 through 132 removed outlier: 7.339A pdb=" N GLU A 167 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 175 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER A 177 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 201 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR A 179 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N TYR A 199 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU A 181 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A 197 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA A 183 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 195 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 157 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A 151 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 128 through 132 removed outlier: 7.302A pdb=" N GLU B 167 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 175 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 176 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR B 178 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 142 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE B 151 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N HIS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 128 through 132 removed outlier: 7.302A pdb=" N GLU B 167 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 175 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 176 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR B 178 " --> pdb=" O TYR B 199 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1185 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: 1.35 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3040 1.34 - 1.46: 2448 1.46 - 1.58: 4396 1.58 - 1.70: 2 1.70 - 1.82: 66 Bond restraints: 9952 Sorted by residual: bond pdb=" CBJ 1PX B 301 " pdb=" OBL 1PX B 301 " ideal model delta sigma weight residual 1.416 1.348 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" CBJ 1PX A 301 " pdb=" OBL 1PX A 301 " ideal model delta sigma weight residual 1.416 1.348 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" N ILE C 110 " pdb=" CA ILE C 110 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.00e+00 bond pdb=" N ARG E 112 " pdb=" CA ARG E 112 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.23e-02 6.61e+03 7.94e+00 bond pdb=" N ARG C 112 " pdb=" CA ARG C 112 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.87e+00 ... (remaining 9947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 13457 2.88 - 5.75: 55 5.75 - 8.63: 18 8.63 - 11.50: 12 11.50 - 14.38: 6 Bond angle restraints: 13548 Sorted by residual: angle pdb=" OAD 1PX B 301 " pdb=" PBP 1PX B 301 " pdb=" OBL 1PX B 301 " ideal model delta sigma weight residual 102.13 87.75 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" OAD 1PX A 301 " pdb=" PBP 1PX A 301 " pdb=" OBL 1PX A 301 " ideal model delta sigma weight residual 102.13 87.91 14.22 3.00e+00 1.11e-01 2.25e+01 angle pdb=" CBJ 1PX B 301 " pdb=" CBO 1PX B 301 " pdb=" NBK 1PX B 301 " ideal model delta sigma weight residual 108.38 94.45 13.93 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CBO 1PX A 301 " pdb=" CBJ 1PX A 301 " pdb=" OBL 1PX A 301 " ideal model delta sigma weight residual 112.59 99.43 13.16 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CBJ 1PX A 301 " pdb=" CBO 1PX A 301 " pdb=" NBK 1PX A 301 " ideal model delta sigma weight residual 108.38 95.23 13.15 3.00e+00 1.11e-01 1.92e+01 ... (remaining 13543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 5729 24.39 - 48.77: 167 48.77 - 73.16: 17 73.16 - 97.54: 2 97.54 - 121.93: 1 Dihedral angle restraints: 5916 sinusoidal: 2312 harmonic: 3604 Sorted by residual: dihedral pdb=" CB CYS F 140 " pdb=" SG CYS F 140 " pdb=" SG CYS F 195 " pdb=" CB CYS F 195 " ideal model delta sinusoidal sigma weight residual 93.00 53.01 39.99 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 195 " pdb=" CB CYS D 195 " ideal model delta sinusoidal sigma weight residual 93.00 53.03 39.97 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CAV 1PX B 301 " pdb=" CAY 1PX B 301 " pdb=" CBA 1PX B 301 " pdb=" CAX 1PX B 301 " ideal model delta sinusoidal sigma weight residual 59.41 -62.52 121.93 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 5913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1477 0.105 - 0.210: 51 0.210 - 0.315: 2 0.315 - 0.420: 0 0.420 - 0.525: 2 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CBO 1PX A 301 " pdb=" CBJ 1PX A 301 " pdb=" CBN 1PX A 301 " pdb=" NBK 1PX A 301 " both_signs ideal model delta sigma weight residual False -2.50 -3.02 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CBO 1PX B 301 " pdb=" CBJ 1PX B 301 " pdb=" CBN 1PX B 301 " pdb=" NBK 1PX B 301 " both_signs ideal model delta sigma weight residual False -2.50 -3.01 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CBN 1PX B 301 " pdb=" CAI 1PX B 301 " pdb=" CBO 1PX B 301 " pdb=" OAE 1PX B 301 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1529 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F 188 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO F 189 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 188 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO D 189 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 189 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 189 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 109 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C GLU C 109 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU C 109 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE C 110 " -0.010 2.00e-02 2.50e+03 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 2915 2.83 - 3.40: 9836 3.40 - 3.98: 19041 3.98 - 4.56: 25612 4.56 - 5.14: 40041 Nonbonded interactions: 97445 Sorted by model distance: nonbonded pdb=" OG SER D 190 " pdb=" OE1 GLU D 191 " model vdw 2.246 3.040 nonbonded pdb=" OG SER F 190 " pdb=" OE1 GLU F 191 " model vdw 2.247 3.040 nonbonded pdb=" O TYR C 190 " pdb=" OH TYR C 196 " model vdw 2.255 3.040 nonbonded pdb=" O TYR E 190 " pdb=" OH TYR E 196 " model vdw 2.256 3.040 nonbonded pdb=" O GLU A 137 " pdb=" OH TYR A 179 " model vdw 2.267 3.040 ... (remaining 97440 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 : 0.003 0.068 9960 Z= 0.188 Angle : 0.723 14.381 13564 Z= 0.338 Chirality : 0.048 0.525 1532 Planarity : 0.004 0.048 1698 Dihedral : 11.157 121.930 3584 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.03 % Allowed : 2.52 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1228 helix: -0.64 (0.33), residues: 190 sheet: -0.09 (0.23), residues: 518 loop : -0.32 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.009 0.001 TYR A 199 PHE 0.007 0.001 PHE E 122 TRP 0.010 0.001 TRP C 167 HIS 0.002 0.000 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.19 ( 9952) covalent geometry : angle 0.72356 / 0.34 (13548) SS BOND : bond 0.00297 / 0.15 ( 8) SS BOND : angle 0.50012 / 0.28 ( 16) hydrogen bonds : bond 0.19775 / 13.11 ( 434) hydrogen bonds : angle 9.00661 / 6.14 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.337 Fit side-chains REVERT: C 97 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7348 (tt0) REVERT: C 179 MET cc_start: 0.8494 (ttp) cc_final: 0.8062 (ttp) REVERT: D 11 LEU cc_start: 0.8542 (tp) cc_final: 0.8323 (tp) REVERT: D 170 LEU cc_start: 0.7634 (tp) cc_final: 0.7389 (tp) REVERT: E 24 LYS cc_start: 0.7809 (mttt) cc_final: 0.7596 (tttp) REVERT: E 30 ASP cc_start: 0.7699 (m-30) cc_final: 0.6961 (p0) REVERT: E 97 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7372 (tt0) REVERT: E 171 ASP cc_start: 0.7917 (t0) cc_final: 0.7422 (t0) REVERT: E 179 MET cc_start: 0.8053 (ttp) cc_final: 0.7160 (ttt) REVERT: A 35 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.5953 (mt) REVERT: A 134 LEU cc_start: 0.9136 (mt) cc_final: 0.8860 (mm) REVERT: A 150 ARG cc_start: 0.8149 (ptm160) cc_final: 0.7200 (ptp-170) REVERT: A 185 GLN cc_start: 0.6863 (tt0) cc_final: 0.6321 (pt0) REVERT: B 35 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6495 (tt) REVERT: B 84 MET cc_start: 0.7860 (mmt) cc_final: 0.7467 (mmt) REVERT: B 150 ARG cc_start: 0.8252 (ptm160) cc_final: 0.6934 (ptp-170) REVERT: B 185 GLN cc_start: 0.7483 (tt0) cc_final: 0.6816 (pt0) outliers start: 11 outliers final: 6 residues processed: 167 average time/residue: 0.0873 time to fit residues: 20.6975 Evaluate side-chains 131 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain B residue 35 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN D 100 ASN E 38 ASN E 96 ASN F 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.211194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.156619 restraints weight = 10129.997| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.19 r_work: 0.3497 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9960 Z= 0.264 Angle : 0.616 7.416 13564 Z= 0.321 Chirality : 0.046 0.151 1532 Planarity : 0.005 0.081 1698 Dihedral : 8.596 87.232 1423 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.77 % Allowed : 9.51 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1228 helix: 0.17 (0.36), residues: 194 sheet: -0.12 (0.23), residues: 472 loop : -0.23 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 146 TYR 0.020 0.002 TYR C 36 PHE 0.031 0.002 PHE A 193 TRP 0.020 0.002 TRP F 47 HIS 0.005 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.26 ( 9952) covalent geometry : angle 0.61636 / 0.32 (13548) SS BOND : bond 0.00205 / 0.10 ( 8) SS BOND : angle 0.60983 / 0.28 ( 16) hydrogen bonds : bond 0.04345 / 2.85 ( 434) hydrogen bonds : angle 6.30095 / 4.31 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: C 179 MET cc_start: 0.8582 (ttp) cc_final: 0.8338 (ttp) REVERT: D 13 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7835 (mmmt) REVERT: D 170 LEU cc_start: 0.7781 (tp) cc_final: 0.7420 (tp) REVERT: E 24 LYS cc_start: 0.7680 (mttt) cc_final: 0.7427 (tttp) REVERT: E 30 ASP cc_start: 0.7830 (m-30) cc_final: 0.7194 (p0) REVERT: E 32 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6846 (m-30) REVERT: E 97 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7475 (tt0) REVERT: E 179 MET cc_start: 0.8349 (ttp) cc_final: 0.7616 (ttp) REVERT: A 115 GLU cc_start: 0.7622 (pt0) cc_final: 0.7326 (pt0) REVERT: A 150 ARG cc_start: 0.8453 (ptm160) cc_final: 0.7773 (ptp-170) REVERT: A 185 GLN cc_start: 0.7695 (tt0) cc_final: 0.7370 (pt0) REVERT: B 84 MET cc_start: 0.8216 (mmt) cc_final: 0.7922 (mmt) REVERT: B 150 ARG cc_start: 0.8236 (ptm160) cc_final: 0.7575 (ptp-170) REVERT: B 185 GLN cc_start: 0.7733 (tt0) cc_final: 0.7344 (pt0) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 0.0901 time to fit residues: 19.1162 Evaluate side-chains 133 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 97 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 30.0000 chunk 22 optimal weight: 0.1980 chunk 100 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 110 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN D 39 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.219560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.160589 restraints weight = 10013.258| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.89 r_work: 0.3651 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9960 Z= 0.106 Angle : 0.494 6.750 13564 Z= 0.259 Chirality : 0.042 0.146 1532 Planarity : 0.004 0.078 1698 Dihedral : 7.857 89.006 1413 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.87 % Allowed : 12.03 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1228 helix: 0.64 (0.36), residues: 206 sheet: 0.13 (0.23), residues: 490 loop : -0.24 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 65 TYR 0.019 0.001 TYR D 60 PHE 0.010 0.001 PHE F 146 TRP 0.012 0.001 TRP B 58 HIS 0.004 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9952) covalent geometry : angle 0.49400 / 0.26 (13548) SS BOND : bond 0.00269 / 0.14 ( 8) SS BOND : angle 0.52859 / 0.25 ( 16) hydrogen bonds : bond 0.03243 / 2.12 ( 434) hydrogen bonds : angle 5.49956 / 3.76 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.357 Fit side-chains REVERT: C 179 MET cc_start: 0.8568 (ttp) cc_final: 0.8295 (ttp) REVERT: D 13 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7861 (mmmt) REVERT: E 30 ASP cc_start: 0.7630 (m-30) cc_final: 0.7062 (p0) REVERT: E 32 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6703 (m-30) REVERT: E 179 MET cc_start: 0.8404 (ttp) cc_final: 0.7663 (ttp) REVERT: A 115 GLU cc_start: 0.7620 (pt0) cc_final: 0.7396 (pt0) REVERT: A 150 ARG cc_start: 0.8260 (ptm160) cc_final: 0.7651 (ptp-170) REVERT: A 185 GLN cc_start: 0.7629 (tt0) cc_final: 0.7376 (pt0) REVERT: B 84 MET cc_start: 0.8176 (mmt) cc_final: 0.7847 (mmt) REVERT: B 150 ARG cc_start: 0.7971 (ptm160) cc_final: 0.7709 (ptt90) REVERT: B 185 GLN cc_start: 0.7558 (tt0) cc_final: 0.7263 (pt0) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 0.0822 time to fit residues: 16.9508 Evaluate side-chains 134 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.0010 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 164 HIS E 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.216664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164206 restraints weight = 10160.374| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.07 r_work: 0.3579 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9960 Z= 0.144 Angle : 0.509 6.710 13564 Z= 0.264 Chirality : 0.043 0.147 1532 Planarity : 0.004 0.080 1698 Dihedral : 7.755 88.709 1413 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.15 % Allowed : 13.71 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1228 helix: 1.00 (0.37), residues: 194 sheet: 0.21 (0.23), residues: 508 loop : -0.05 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 198 TYR 0.022 0.001 TYR D 60 PHE 0.010 0.001 PHE A 193 TRP 0.013 0.001 TRP B 31 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 9952) covalent geometry : angle 0.50921 / 0.26 (13548) SS BOND : bond 0.00243 / 0.13 ( 8) SS BOND : angle 0.61785 / 0.30 ( 16) hydrogen bonds : bond 0.03173 / 2.08 ( 434) hydrogen bonds : angle 5.37536 / 3.69 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.413 Fit side-chains REVERT: D 13 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7909 (mmmt) REVERT: E 30 ASP cc_start: 0.7646 (m-30) cc_final: 0.7100 (p0) REVERT: E 32 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6703 (m-30) REVERT: E 179 MET cc_start: 0.8506 (ttp) cc_final: 0.7752 (ttp) REVERT: A 150 ARG cc_start: 0.8293 (ptm160) cc_final: 0.7758 (ptp-170) REVERT: A 158 ARG cc_start: 0.8253 (tpt170) cc_final: 0.8013 (tpt90) REVERT: A 185 GLN cc_start: 0.7684 (tt0) cc_final: 0.7443 (pt0) REVERT: B 84 MET cc_start: 0.8193 (mmt) cc_final: 0.7915 (mmt) REVERT: B 150 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7713 (ptt90) REVERT: B 185 GLN cc_start: 0.7615 (tt0) cc_final: 0.7336 (pt0) outliers start: 23 outliers final: 15 residues processed: 139 average time/residue: 0.1003 time to fit residues: 20.2064 Evaluate side-chains 138 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 0.0770 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 6 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.218546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.165164 restraints weight = 10130.309| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.29 r_work: 0.3584 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9960 Z= 0.119 Angle : 0.489 7.292 13564 Z= 0.254 Chirality : 0.042 0.139 1532 Planarity : 0.004 0.078 1698 Dihedral : 7.514 86.067 1413 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.61 % Allowed : 13.99 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.25), residues: 1228 helix: 1.18 (0.37), residues: 194 sheet: 0.26 (0.23), residues: 508 loop : 0.01 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.024 0.001 TYR D 60 PHE 0.010 0.001 PHE A 193 TRP 0.011 0.001 TRP B 31 HIS 0.002 0.000 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9952) covalent geometry : angle 0.48935 / 0.25 (13548) SS BOND : bond 0.00252 / 0.13 ( 8) SS BOND : angle 0.60136 / 0.29 ( 16) hydrogen bonds : bond 0.02963 / 1.94 ( 434) hydrogen bonds : angle 5.17097 / 3.56 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.411 Fit side-chains REVERT: D 13 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7957 (mmmt) REVERT: D 170 LEU cc_start: 0.7767 (tp) cc_final: 0.7471 (tp) REVERT: E 30 ASP cc_start: 0.7669 (m-30) cc_final: 0.7083 (p0) REVERT: E 32 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6730 (m-30) REVERT: E 179 MET cc_start: 0.8497 (ttp) cc_final: 0.8080 (ttp) REVERT: A 35 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6386 (mt) REVERT: A 115 GLU cc_start: 0.7735 (pt0) cc_final: 0.7477 (pt0) REVERT: A 150 ARG cc_start: 0.8335 (ptm160) cc_final: 0.7746 (ptp-170) REVERT: A 185 GLN cc_start: 0.7736 (tt0) cc_final: 0.7443 (pt0) REVERT: B 84 MET cc_start: 0.8249 (mmt) cc_final: 0.7973 (mmt) REVERT: B 150 ARG cc_start: 0.7995 (ptm160) cc_final: 0.7727 (ptt90) REVERT: B 185 GLN cc_start: 0.7643 (tt0) cc_final: 0.7346 (pt0) outliers start: 28 outliers final: 18 residues processed: 148 average time/residue: 0.0804 time to fit residues: 17.9397 Evaluate side-chains 145 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 34 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN E 95 ASN E 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.210961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158349 restraints weight = 10110.655| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.49 r_work: 0.3520 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9960 Z= 0.237 Angle : 0.577 7.220 13564 Z= 0.296 Chirality : 0.045 0.150 1532 Planarity : 0.005 0.079 1698 Dihedral : 7.738 83.623 1413 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.24 % Allowed : 14.18 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1228 helix: 0.78 (0.36), residues: 194 sheet: 0.15 (0.23), residues: 504 loop : 0.01 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.024 0.002 TYR D 60 PHE 0.015 0.002 PHE A 193 TRP 0.016 0.002 TRP D 47 HIS 0.004 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 ( 9952) covalent geometry : angle 0.57644 / 0.30 (13548) SS BOND : bond 0.00216 / 0.11 ( 8) SS BOND : angle 0.75297 / 0.37 ( 16) hydrogen bonds : bond 0.03462 / 2.28 ( 434) hydrogen bonds : angle 5.57331 / 3.83 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.354 Fit side-chains REVERT: C 171 ASP cc_start: 0.7658 (t0) cc_final: 0.7457 (t0) REVERT: D 13 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7963 (mmmt) REVERT: E 24 LYS cc_start: 0.7585 (mttt) cc_final: 0.7358 (tttp) REVERT: E 30 ASP cc_start: 0.7799 (m-30) cc_final: 0.7146 (p0) REVERT: E 32 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6815 (m-30) REVERT: E 179 MET cc_start: 0.8573 (ttp) cc_final: 0.8135 (ttp) REVERT: A 115 GLU cc_start: 0.7824 (pt0) cc_final: 0.7547 (pt0) REVERT: A 150 ARG cc_start: 0.8341 (ptm160) cc_final: 0.7686 (ptp-170) REVERT: A 185 GLN cc_start: 0.7748 (tt0) cc_final: 0.7416 (pt0) REVERT: B 84 MET cc_start: 0.8217 (mmt) cc_final: 0.7934 (mmt) REVERT: B 150 ARG cc_start: 0.8052 (ptm160) cc_final: 0.7419 (ptp-170) REVERT: B 185 GLN cc_start: 0.7663 (tt0) cc_final: 0.7305 (pt0) outliers start: 24 outliers final: 16 residues processed: 144 average time/residue: 0.0890 time to fit residues: 18.9010 Evaluate side-chains 135 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 74 optimal weight: 0.0370 chunk 67 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 149 ASN C 202 HIS E 95 ASN E 149 ASN F 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.217621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149268 restraints weight = 10009.867| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.92 r_work: 0.3590 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9960 Z= 0.113 Angle : 0.497 7.735 13564 Z= 0.258 Chirality : 0.042 0.142 1532 Planarity : 0.004 0.080 1698 Dihedral : 7.200 81.906 1411 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.15 % Allowed : 14.46 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1228 helix: 1.14 (0.37), residues: 194 sheet: 0.19 (0.23), residues: 508 loop : 0.09 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 65 TYR 0.020 0.001 TYR D 60 PHE 0.008 0.001 PHE A 193 TRP 0.013 0.001 TRP B 58 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 9952) covalent geometry : angle 0.49743 / 0.26 (13548) SS BOND : bond 0.00267 / 0.14 ( 8) SS BOND : angle 0.52851 / 0.27 ( 16) hydrogen bonds : bond 0.02912 / 1.90 ( 434) hydrogen bonds : angle 5.16352 / 3.55 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.346 Fit side-chains REVERT: C 171 ASP cc_start: 0.7769 (t0) cc_final: 0.7543 (t0) REVERT: D 13 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7963 (mmmt) REVERT: D 60 TYR cc_start: 0.9131 (m-80) cc_final: 0.8849 (m-80) REVERT: E 30 ASP cc_start: 0.7668 (m-30) cc_final: 0.7102 (p0) REVERT: E 32 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: E 179 MET cc_start: 0.8574 (ttp) cc_final: 0.7776 (ttp) REVERT: F 60 TYR cc_start: 0.9180 (m-80) cc_final: 0.8913 (m-80) REVERT: A 150 ARG cc_start: 0.8269 (ptm160) cc_final: 0.7644 (ptp-170) REVERT: A 185 GLN cc_start: 0.7772 (tt0) cc_final: 0.7407 (pt0) REVERT: B 84 MET cc_start: 0.8184 (mmt) cc_final: 0.7898 (mmt) REVERT: B 150 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7674 (ptt90) REVERT: B 185 GLN cc_start: 0.7611 (tt0) cc_final: 0.7288 (pt0) outliers start: 23 outliers final: 16 residues processed: 141 average time/residue: 0.0823 time to fit residues: 17.5190 Evaluate side-chains 136 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 60 optimal weight: 40.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.212046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.158896 restraints weight = 10175.890| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.39 r_work: 0.3522 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9960 Z= 0.206 Angle : 0.561 7.595 13564 Z= 0.288 Chirality : 0.044 0.146 1532 Planarity : 0.005 0.080 1698 Dihedral : 7.358 81.613 1411 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.87 % Allowed : 14.74 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1228 helix: 0.90 (0.36), residues: 194 sheet: 0.16 (0.23), residues: 504 loop : 0.09 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.021 0.002 TYR D 60 PHE 0.013 0.001 PHE A 193 TRP 0.014 0.002 TRP B 31 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 9952) covalent geometry : angle 0.56109 / 0.29 (13548) SS BOND : bond 0.00219 / 0.11 ( 8) SS BOND : angle 0.71608 / 0.37 ( 16) hydrogen bonds : bond 0.03227 / 2.12 ( 434) hydrogen bonds : angle 5.37866 / 3.71 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.352 Fit side-chains REVERT: C 171 ASP cc_start: 0.7809 (t0) cc_final: 0.7588 (t0) REVERT: D 13 LYS cc_start: 0.8205 (mmmt) cc_final: 0.8003 (mmmt) REVERT: D 60 TYR cc_start: 0.9181 (m-80) cc_final: 0.8913 (m-80) REVERT: E 30 ASP cc_start: 0.7766 (m-30) cc_final: 0.7171 (p0) REVERT: E 32 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6765 (m-30) REVERT: E 179 MET cc_start: 0.8632 (ttp) cc_final: 0.8203 (ttp) REVERT: F 60 TYR cc_start: 0.9231 (m-80) cc_final: 0.8977 (m-80) REVERT: A 150 ARG cc_start: 0.8306 (ptm160) cc_final: 0.7675 (ptp-170) REVERT: A 185 GLN cc_start: 0.7845 (tt0) cc_final: 0.7447 (pt0) REVERT: B 84 MET cc_start: 0.8236 (mmt) cc_final: 0.7947 (mmt) REVERT: B 150 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7409 (ptp-170) REVERT: B 185 GLN cc_start: 0.7707 (tt0) cc_final: 0.7326 (pt0) outliers start: 20 outliers final: 16 residues processed: 135 average time/residue: 0.0859 time to fit residues: 17.2887 Evaluate side-chains 127 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 72 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 119 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 164 HIS E 95 ASN F 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.216890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158199 restraints weight = 10019.833| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.85 r_work: 0.3588 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9960 Z= 0.128 Angle : 0.518 8.813 13564 Z= 0.267 Chirality : 0.042 0.144 1532 Planarity : 0.004 0.081 1698 Dihedral : 7.114 80.251 1411 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.77 % Allowed : 15.86 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1228 helix: 1.14 (0.37), residues: 194 sheet: 0.22 (0.23), residues: 504 loop : 0.15 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 200 TYR 0.020 0.001 TYR D 60 PHE 0.009 0.001 PHE A 193 TRP 0.013 0.001 TRP B 31 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9952) covalent geometry : angle 0.51832 / 0.27 (13548) SS BOND : bond 0.00241 / 0.13 ( 8) SS BOND : angle 0.57375 / 0.30 ( 16) hydrogen bonds : bond 0.02932 / 1.92 ( 434) hydrogen bonds : angle 5.14275 / 3.55 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.328 Fit side-chains REVERT: D 60 TYR cc_start: 0.9089 (m-80) cc_final: 0.8783 (m-80) REVERT: E 30 ASP cc_start: 0.7642 (m-30) cc_final: 0.7131 (p0) REVERT: E 32 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: E 179 MET cc_start: 0.8726 (ttp) cc_final: 0.8299 (ttp) REVERT: F 60 TYR cc_start: 0.9140 (m-80) cc_final: 0.8852 (m-80) REVERT: A 150 ARG cc_start: 0.8153 (ptm160) cc_final: 0.7693 (ptp-170) REVERT: A 185 GLN cc_start: 0.7778 (tt0) cc_final: 0.7484 (pt0) REVERT: B 84 MET cc_start: 0.8137 (mmt) cc_final: 0.7881 (mmt) REVERT: B 150 ARG cc_start: 0.7928 (ptm160) cc_final: 0.7663 (ptt90) REVERT: B 185 GLN cc_start: 0.7607 (tt0) cc_final: 0.7348 (pt0) outliers start: 19 outliers final: 17 residues processed: 125 average time/residue: 0.0773 time to fit residues: 14.6709 Evaluate side-chains 134 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 15 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 164 HIS E 95 ASN F 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.216949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.164717 restraints weight = 10059.481| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.67 r_work: 0.3587 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9960 Z= 0.134 Angle : 0.521 9.803 13564 Z= 0.266 Chirality : 0.043 0.141 1532 Planarity : 0.004 0.081 1698 Dihedral : 7.059 79.618 1411 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.05 % Allowed : 15.02 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1228 helix: 1.18 (0.37), residues: 194 sheet: 0.25 (0.23), residues: 504 loop : 0.18 (0.30), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 200 TYR 0.020 0.001 TYR D 60 PHE 0.010 0.001 PHE A 193 TRP 0.013 0.001 TRP B 31 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 9952) covalent geometry : angle 0.52083 / 0.27 (13548) SS BOND : bond 0.00213 / 0.11 ( 8) SS BOND : angle 0.57459 / 0.29 ( 16) hydrogen bonds : bond 0.02940 / 1.93 ( 434) hydrogen bonds : angle 5.09251 / 3.51 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.351 Fit side-chains REVERT: C 171 ASP cc_start: 0.7943 (t0) cc_final: 0.7703 (t0) REVERT: D 60 TYR cc_start: 0.9087 (m-80) cc_final: 0.8774 (m-80) REVERT: E 30 ASP cc_start: 0.7648 (m-30) cc_final: 0.7131 (p0) REVERT: E 32 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6697 (m-30) REVERT: E 179 MET cc_start: 0.8684 (ttp) cc_final: 0.8265 (ttp) REVERT: F 60 TYR cc_start: 0.9150 (m-80) cc_final: 0.8914 (m-80) REVERT: A 150 ARG cc_start: 0.8227 (ptm160) cc_final: 0.7782 (ptp-170) REVERT: A 185 GLN cc_start: 0.7849 (tt0) cc_final: 0.7528 (pt0) REVERT: B 84 MET cc_start: 0.8170 (mmt) cc_final: 0.7920 (mmt) REVERT: B 185 GLN cc_start: 0.7686 (tt0) cc_final: 0.7417 (pt0) outliers start: 22 outliers final: 16 residues processed: 127 average time/residue: 0.0804 time to fit residues: 15.5384 Evaluate side-chains 130 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 94 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 164 HIS E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.216060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165169 restraints weight = 10068.268| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.84 r_work: 0.3570 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9960 Z= 0.155 Angle : 0.531 9.586 13564 Z= 0.271 Chirality : 0.043 0.143 1532 Planarity : 0.004 0.079 1698 Dihedral : 7.066 79.340 1411 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.77 % Allowed : 15.76 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1228 helix: 1.12 (0.36), residues: 194 sheet: 0.24 (0.23), residues: 504 loop : 0.21 (0.30), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 200 TYR 0.021 0.001 TYR D 60 PHE 0.011 0.001 PHE A 193 TRP 0.013 0.001 TRP B 31 HIS 0.002 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9952) covalent geometry : angle 0.53126 / 0.27 (13548) SS BOND : bond 0.00229 / 0.12 ( 8) SS BOND : angle 0.60504 / 0.31 ( 16) hydrogen bonds : bond 0.02989 / 1.96 ( 434) hydrogen bonds : angle 5.14520 / 3.55 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.32 seconds wall clock time: 51 minutes 49.04 seconds (3109.04 seconds total)