Starting phenix.real_space_refine on Thu Jun 4 19:42:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7e_70196/06_2026/9o7e_70196.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7e_70196/06_2026/9o7e_70196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o7e_70196/06_2026/9o7e_70196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7e_70196/06_2026/9o7e_70196.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o7e_70196/06_2026/9o7e_70196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7e_70196/06_2026/9o7e_70196.map" } resolution = 3.9 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= 0.032 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: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 4670 2.51 5 N 1567 2.21 5 O 1709 1.98 5 H 6620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14593 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1002 Classifications: {'peptide': 167} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 160} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 742 Unresolved non-hydrogen angles: 1055 Unresolved non-hydrogen dihedrals: 486 Unresolved non-hydrogen chiralities: 197 Planarities with less than four sites: {'ARG:plan': 15, 'TRP:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 22, 'HIS:plan': 7, 'GLN:plan1': 8, 'TYR:plan': 4, 'ASP:plan': 14, 'PHE:plan': 4, 'TYR%COO:plan': 1} Unresolved non-hydrogen planarities: 397 Chain: "E" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1356 Classifications: {'peptide': 224} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 818 Unresolved non-hydrogen angles: 1205 Unresolved non-hydrogen dihedrals: 528 Unresolved non-hydrogen chiralities: 263 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 5, 'TYR:plan': 11, 'PHE:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 5, 'ARG:plan': 5, 'ASP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 352 Chain: "F" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1301 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 199} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 766 Unresolved non-hydrogen angles: 1134 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 257 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 7, 'TYR:plan': 9, 'TRP:plan': 4, 'ASP:plan': 7, 'ARG:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 300 Chain: "B" Number of atoms: 4487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4487 Classifications: {'peptide': 278} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain: "C" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3301 Classifications: {'peptide': 224} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "D" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3146 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 199} Time building chain proxies: 3.15, per 1000 atoms: 0.22 Number of scatterers: 14593 At special positions: 0 Unit cell: (97.578, 110.922, 168.468, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 1709 8.00 N 1567 7.00 C 4670 6.00 H 6620 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 100 " distance=2.02 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 211 " distance=2.02 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 104 " distance=2.06 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 213 " 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: 1.19 Conformation dependent library (CDL) restraints added in 455.3 milliseconds 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1334 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 25 sheets defined 31.0% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 137 through 158 Processing helix chain 'A' and resid 158 through 163 removed outlier: 4.295A pdb=" N SER A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 189 through 217 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 66 through 69 removed outlier: 3.593A pdb=" N GLN E 69 " --> pdb=" O GLN E 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 66 through 69' Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 202 through 207 removed outlier: 4.306A pdb=" N GLY E 205 " --> pdb=" O SER E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 219 Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 201 through 208 Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 41 through 56 Processing helix chain 'B' and resid 59 through 72 removed outlier: 4.329A pdb=" N TYR B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 109 through 127 Processing helix chain 'B' and resid 134 through 184 removed outlier: 3.840A pdb=" N HIS B 184 " --> pdb=" O CYS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 224 removed outlier: 3.663A pdb=" N LYS B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 66 through 69 removed outlier: 3.725A pdb=" N GLN C 69 " --> pdb=" O GLN C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 69' Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 216 through 219 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 201 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 251 through 253 removed outlier: 3.593A pdb=" N ILE A 281 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AA3, first strand: chain 'E' and resid 14 through 16 removed outlier: 4.190A pdb=" N GLY E 37 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR E 36 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER E 56 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE E 38 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TRP E 54 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TRP E 40 " --> pdb=" O MET E 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 14 through 16 removed outlier: 7.015A pdb=" N CYS E 100 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TRP E 118 " --> pdb=" O CYS E 100 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG E 102 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 135 through 139 removed outlier: 6.174A pdb=" N TYR E 191 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 135 through 139 removed outlier: 6.174A pdb=" N TYR E 191 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 166 through 169 Processing sheet with id=AA8, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.642A pdb=" N VAL F 25 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP F 51 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.642A pdb=" N VAL F 25 " --> pdb=" O THR F 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 33 through 38 Processing sheet with id=AB2, first strand: chain 'F' and resid 134 through 138 removed outlier: 4.829A pdb=" N THR F 151 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU F 200 " --> pdb=" O THR F 151 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL F 153 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU F 198 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU F 155 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER F 196 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER F 157 " --> pdb=" O ALA F 194 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA F 194 " --> pdb=" O SER F 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 134 through 138 removed outlier: 4.829A pdb=" N THR F 151 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU F 200 " --> pdb=" O THR F 151 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL F 153 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU F 198 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU F 155 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER F 196 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER F 157 " --> pdb=" O ALA F 194 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA F 194 " --> pdb=" O SER F 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 173 through 175 removed outlier: 4.231A pdb=" N TRP F 168 " --> pdb=" O VAL F 175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 251 through 253 Processing sheet with id=AB6, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AB7, first strand: chain 'C' and resid 14 through 16 removed outlier: 4.317A pdb=" N GLY C 37 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE C 38 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP C 54 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP C 40 " --> pdb=" O MET C 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 135 through 139 removed outlier: 6.171A pdb=" N TYR C 191 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 146 through 147 removed outlier: 6.171A pdb=" N TYR C 191 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 166 through 169 Processing sheet with id=AC2, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.697A pdb=" N VAL D 25 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 100 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP D 51 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.697A pdb=" N VAL D 25 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 100 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 33 through 38 Processing sheet with id=AC5, first strand: chain 'D' and resid 134 through 138 removed outlier: 3.546A pdb=" N VAL D 153 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR D 151 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU D 200 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL D 153 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU D 198 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU D 155 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER D 196 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER D 157 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA D 194 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 134 through 138 removed outlier: 3.546A pdb=" N VAL D 153 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR D 151 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU D 200 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL D 153 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU D 198 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU D 155 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER D 196 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER D 157 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA D 194 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 173 through 175 removed outlier: 4.475A pdb=" N TRP D 168 " --> pdb=" O VAL D 175 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1425 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: 3.43 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.08: 1994 1.08 - 1.27: 6166 1.27 - 1.45: 2149 1.45 - 1.64: 4363 1.64 - 1.82: 37 Bond restraints: 14709 Sorted by residual: bond pdb=" CD1 PHE B 131 " pdb=" HD1 PHE B 131 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" CZ3 TRP C 169 " pdb=" HZ3 TRP C 169 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" CD2 PHE B 98 " pdb=" HD2 PHE B 98 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" CD1 PHE C 99 " pdb=" HD1 PHE C 99 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" CE2 PHE B 98 " pdb=" HE2 PHE B 98 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.52e+01 ... (remaining 14704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 21471 2.61 - 5.22: 2815 5.22 - 7.83: 1136 7.83 - 10.44: 24 10.44 - 13.05: 9 Bond angle restraints: 25455 Sorted by residual: angle pdb=" N PHE B 237 " pdb=" CA PHE B 237 " pdb=" C PHE B 237 " ideal model delta sigma weight residual 112.24 118.36 -6.12 1.28e+00 6.10e-01 2.29e+01 angle pdb=" C TYR C 36 " pdb=" N GLY C 37 " pdb=" CA GLY C 37 " ideal model delta sigma weight residual 120.60 125.14 -4.54 1.01e+00 9.80e-01 2.02e+01 angle pdb=" C GLU B 242 " pdb=" N PRO B 243 " pdb=" CA PRO B 243 " ideal model delta sigma weight residual 119.76 124.26 -4.50 1.03e+00 9.43e-01 1.91e+01 angle pdb=" C MET B 73 " pdb=" CA MET B 73 " pdb=" CB MET B 73 " ideal model delta sigma weight residual 116.54 110.23 6.31 1.46e+00 4.69e-01 1.87e+01 angle pdb=" C PHE B 131 " pdb=" N GLY B 132 " pdb=" CA GLY B 132 " ideal model delta sigma weight residual 119.92 124.00 -4.08 9.60e-01 1.09e+00 1.81e+01 ... (remaining 25450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 6109 16.87 - 33.75: 208 33.75 - 50.62: 104 50.62 - 67.50: 50 67.50 - 84.37: 3 Dihedral angle restraints: 6474 sinusoidal: 3461 harmonic: 3013 Sorted by residual: dihedral pdb=" CA PRO D 133 " pdb=" C PRO D 133 " pdb=" N SER D 134 " pdb=" CA SER D 134 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TYR F 103 " pdb=" C TYR F 103 " pdb=" N CYS F 104 " pdb=" CA CYS F 104 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA THR D 112 " pdb=" C THR D 112 " pdb=" N ALA D 113 " pdb=" CA ALA D 113 " ideal model delta harmonic sigma weight residual 180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 6471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 575 0.056 - 0.111: 165 0.111 - 0.167: 78 0.167 - 0.222: 21 0.222 - 0.278: 5 Chirality restraints: 844 Sorted by residual: chirality pdb=" CA ASP D 158 " pdb=" N ASP D 158 " pdb=" C ASP D 158 " pdb=" CB ASP D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ASN D 190 " pdb=" N ASN D 190 " pdb=" C ASN D 190 " pdb=" CB ASN D 190 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN D 43 " pdb=" N ASN D 43 " pdb=" C ASN D 43 " pdb=" CB ASN D 43 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 841 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 115 " 0.152 2.00e-02 2.50e+03 5.95e-02 1.06e+02 pdb=" CG PHE C 115 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE C 115 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE C 115 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE C 115 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 115 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE C 115 " 0.012 2.00e-02 2.50e+03 pdb=" HD1 PHE C 115 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 PHE C 115 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 PHE C 115 " 0.044 2.00e-02 2.50e+03 pdb=" HE2 PHE C 115 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE C 115 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 187 " 0.066 2.00e-02 2.50e+03 6.24e-02 5.84e+01 pdb=" CD GLN D 187 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLN D 187 " -0.040 2.00e-02 2.50e+03 pdb=" NE2 GLN D 187 " -0.062 2.00e-02 2.50e+03 pdb="HE21 GLN D 187 " 0.105 2.00e-02 2.50e+03 pdb="HE22 GLN D 187 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 63 " 0.092 2.00e-02 2.50e+03 3.81e-02 4.35e+01 pdb=" CG TYR B 63 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR B 63 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 63 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 63 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 63 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 63 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 63 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR B 63 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR B 63 " -0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR B 63 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR B 63 " -0.008 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1594 2.26 - 2.85: 26982 2.85 - 3.43: 35118 3.43 - 4.02: 45574 4.02 - 4.60: 65367 Nonbonded interactions: 174635 Sorted by model distance: nonbonded pdb=" HG SER D 212 " pdb=" OE2 GLU D 223 " model vdw 1.681 2.450 nonbonded pdb=" HG SER C 143 " pdb=" OXT SER D 232 " model vdw 1.690 2.450 nonbonded pdb=" OE2 GLU D 144 " pdb=" HG1 THR D 151 " model vdw 1.693 2.450 nonbonded pdb=" O ALA B 79 " pdb=" HG CYS B 83 " model vdw 1.695 2.620 nonbonded pdb=" O ILE B 235 " pdb=" HG SER B 236 " model vdw 1.703 2.450 ... (remaining 174630 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 6 and (name N or name CA or name C or name O or name H1 o \ r name HA )) or (resid 7 through 11 and (name N or name CA or name C or name O o \ r name H or name HA )) or resid 12 or (resid 13 through 17 and (name N or name C \ A or name C or name O or name H or name HA )) or (resid 18 and (name N or name C \ A or name C or name O or name HA )) or resid 19 or (resid 20 through 29 and (nam \ e N or name CA or name C or name O or name H or name HA )) or resid 30 or (resid \ 31 through 36 and (name N or name CA or name C or name O or name H or name HA ) \ ) or resid 37 or (resid 38 through 44 and (name N or name CA or name C or name O \ or name H or name HA )) or (resid 45 and (name N or name CA or name C or name O \ or name HA )) or resid 46 or (resid 47 and (name N or name CA or name C or name \ O or name H or name HA )) or resid 48 or (resid 49 through 52 and (name N or na \ me CA or name C or name O or name H or name HA )) or resid 53 or (resid 54 throu \ gh 59 and (name N or name CA or name C or name O or name H or name HA )) or resi \ d 60 or (resid 61 through 69 and (name N or name CA or name C or name O or name \ H or name HA )) or resid 70 or (resid 71 through 103 and (name N or name CA or n \ ame C or name O or name H or name HA )) or resid 104 or (resid 105 through 106 a \ nd (name N or name CA or name C or name O or name H or name HA )) or resid 107 o \ r (resid 108 through 112 and (name N or name CA or name C or name O or name H or \ name HA )) or resid 113 or (resid 114 through 118 and (name N or name CA or nam \ e C or name O or name H or name HA )) or resid 119 or (resid 120 and (name N or \ name CA or name C or name O or name H or name HA )) or resid 121 or (resid 122 t \ hrough 132 and (name N or name CA or name C or name O or name H or name HA )) or \ resid 133 or (resid 134 and (name N or name CA or name C or name O or name HA ) \ ) or (resid 135 through 137 and (name N or name CA or name C or name O or name H \ or name HA )) or (resid 138 and (name N or name CA or name C or name O or name \ HA )) or (resid 139 through 140 and (name N or name CA or name C or name O or na \ me H or name HA )) or (resid 141 and (name N or name CA or name C or name O or n \ ame HA )) or (resid 142 through 147 and (name N or name CA or name C or name O o \ r name H or name HA )) or resid 148 through 149 or (resid 150 through 153 and (n \ ame N or name CA or name C or name O or name H or name HA )) or resid 154 or (re \ sid 155 through 161 and (name N or name CA or name C or name O or name H or name \ HA )) or (resid 162 and (name N or name CA or name C or name O or name HA )) or \ (resid 163 and (name N or name CA or name C or name O or name H or name HA )) o \ r (resid 164 and (name N or name CA or name C or name O or name HA )) or (resid \ 165 through 171 and (name N or name CA or name C or name O or name H or name HA \ )) or resid 172 or (resid 173 through 176 and (name N or name CA or name C or na \ me O or name H or name HA )) or resid 177 or (resid 178 through 181 and (name N \ or name CA or name C or name O or name H or name HA )) or (resid 182 and (name N \ or name CA or name C or name O or name HA )) or (resid 183 through 188 and (nam \ e N or name CA or name C or name O or name H or name HA )) or resid 189 or (resi \ d 190 through 199 and (name N or name CA or name C or name O or name H or name H \ A )) or (resid 200 and (name N or name CA or name C or name O or name HA )) or ( \ resid 201 through 204 and (name N or name CA or name C or name O or name H or na \ me HA )) or resid 205 or (resid 206 through 216 and (name N or name CA or name C \ or name O or name H or name HA )) or (resid 217 and (name N or name CA or name \ C or name O or name HA )) or (resid 218 through 227 and (name N or name CA or na \ me C or name O or name H or name HA )) or (resid 228 and (name N or name CA or n \ ame C or name O or name HA )) or (resid 229 and (name N or name CA or name C or \ name O or name OXT or name H or name HA )))) selection = chain 'E' } ncs_group { reference = (chain 'D' and ((resid 17 and (name N or name CA or name C or name O or name H1 \ or name H2 or name H3 or name HA )) or (resid 18 through 21 and (name N or name \ CA or name C or name O or name H or name HA )) or (resid 22 through 23 and (name \ N or name CA or name C or name O or name HA )) or (resid 24 through 28 and (nam \ e N or name CA or name C or name O or name H or name HA )) or (resid 29 and (nam \ e N or name CA or name C or name O or name HA )) or resid 30 or (resid 31 throug \ h 38 and (name N or name CA or name C or name O or name H or name HA )) or resid \ 39 or (resid 40 through 44 and (name N or name CA or name C or name O or name H \ or name HA )) or resid 45 or (resid 46 through 55 and (name N or name CA or nam \ e C or name O or name H or name HA )) or (resid 56 and (name N or name CA or nam \ e C or name O or name HA )) or resid 57 or (resid 58 through 59 and (name N or n \ ame CA or name C or name O or name H or name HA )) or (resid 60 and (name N or n \ ame CA or name C or name O or name HA )) or (resid 61 through 70 and (name N or \ name CA or name C or name O or name H or name HA )) or (resid 71 and (name N or \ name CA or name C or name O or name HA )) or (resid 72 and (name N or name CA or \ name C or name O or name H or name HA )) or resid 73 or (resid 74 and (name N o \ r name CA or name C or name O or name H or name HA )) or (resid 75 and (name N o \ r name CA or name C or name O or name HA )) or (resid 76 through 79 and (name N \ or name CA or name C or name O or name H or name HA )) or resid 80 or (resid 81 \ through 83 and (name N or name CA or name C or name O or name H or name HA )) or \ resid 84 or (resid 85 through 89 and (name N or name CA or name C or name O or \ name H or name HA )) or resid 90 or (resid 91 through 92 and (name N or name CA \ or name C or name O or name H or name HA )) or resid 93 or (resid 94 through 96 \ and (name N or name CA or name C or name O or name H or name HA )) or resid 97 o \ r (resid 98 through 113 and (name N or name CA or name C or name O or name H or \ name HA )) or resid 114 or (resid 115 through 117 and (name N or name CA or name \ C or name O or name H or name HA )) or resid 118 through 120 or (resid 121 thro \ ugh 126 and (name N or name CA or name C or name O or name H or name HA )) or re \ sid 127 or (resid 128 and (name N or name CA or name C or name O or name H or na \ me HA )) or (resid 129 and (name N or name CA or name C or name O or name HA )) \ or (resid 130 through 132 and (name N or name CA or name C or name O or name H o \ r name HA )) or (resid 133 and (name N or name CA or name C or name O or name HA \ )) or (resid 134 through 138 and (name N or name CA or name C or name O or name \ H or name HA )) or (resid 139 through 140 and (name N or name CA or name C or n \ ame O or name HA )) or (resid 141 through 160 and (name N or name CA or name C o \ r name O or name H or name HA )) or (resid 161 and (name N or name CA or name C \ or name O or name HA )) or resid 162 or (resid 163 through 173 and (name N or na \ me CA or name C or name O or name H or name HA )) or (resid 174 and (name N or n \ ame CA or name C or name O or name HA )) or (resid 175 through 177 and (name N o \ r name CA or name C or name O or name H or name HA )) or resid 178 or (resid 179 \ through 183 and (name N or name CA or name C or name O or name H or name HA )) \ or (resid 184 and (name N or name CA or name C or name O or name HA )) or (resid \ 185 through 201 and (name N or name CA or name C or name O or name H or name HA \ )) or (resid 202 and (name N or name CA or name C or name O or name HA )) or (r \ esid 203 through 218 and (name N or name CA or name C or name O or name H or nam \ e HA )) or resid 219 or (resid 220 through 227 and (name N or name CA or name C \ or name O or name H or name HA )) or (resid 228 and (name N or name CA or name C \ or name O or name HA )) or (resid 229 through 231 and (name N or name CA or nam \ e C or name O or name H or name HA )) or (resid 232 and (name N or name CA or na \ me C or name O or name OXT or name H or name HA )))) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.310 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 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 : 0.012 0.061 8093 Z= 0.788 Angle : 1.444 8.026 10721 Z= 1.000 Chirality : 0.070 0.278 844 Planarity : 0.007 0.053 1610 Dihedral : 9.710 84.374 2690 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.61 % Allowed : 3.43 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.00 (0.22), residues: 1313 helix: 0.89 (0.26), residues: 332 sheet: 1.04 (0.25), residues: 394 loop : 0.42 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 66 TYR 0.078 0.006 TYR B 63 PHE 0.084 0.007 PHE C 115 TRP 0.021 0.003 TRP D 107 HIS 0.012 0.001 HIS D 208 Details of bonding type rmsd/Z covalent geometry : bond 0.01186 / 0.79 ( 8089) covalent geometry : angle 1.44317 / 1.00 (10713) SS BOND : bond 0.01441 / 0.74 ( 4) SS BOND : angle 2.61700 / 1.78 ( 8) hydrogen bonds : bond 0.17727 / 13.96 ( 505) hydrogen bonds : angle 7.29662 / 5.68 ( 1425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 137 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue ALA 142 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue ILE 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue VAL 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue ALA 202 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue TYR 230 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue TYR 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ALA 285 is missing expected H atoms. Skipping. Residue MET 286 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue VAL 289 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue VAL 22 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue TYR 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue TYR 108 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue THR 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue TYR 209 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue SER 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ALA 59 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue TYR 65 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue TYR 103 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue THR 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 166 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue LYS 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue ALA 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 211 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 MET cc_start: 0.5375 (mmm) cc_final: 0.4992 (mtm) REVERT: C 117 ILE cc_start: 0.7464 (mt) cc_final: 0.7238 (tp) REVERT: D 88 THR cc_start: 0.6448 (m) cc_final: 0.6191 (p) REVERT: D 148 ASN cc_start: 0.8131 (m-40) cc_final: 0.7861 (m110) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2181 time to fit residues: 53.5741 Evaluate side-chains 113 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN C 67 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.141291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.113298 restraints weight = 78167.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.111157 restraints weight = 59841.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.112540 restraints weight = 38442.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.114862 restraints weight = 28277.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.114720 restraints weight = 22642.826| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.168 8093 Z= 0.355 Angle : 0.818 8.017 10721 Z= 0.465 Chirality : 0.048 0.175 844 Planarity : 0.006 0.068 1610 Dihedral : 5.752 29.525 1390 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.27 % Favored : 95.20 % Rotamer: Outliers : 2.30 % Allowed : 9.38 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.88 (0.23), residues: 1313 helix: 1.67 (0.26), residues: 335 sheet: 0.52 (0.25), residues: 420 loop : 0.09 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 225 TYR 0.031 0.003 TYR D 52 PHE 0.038 0.004 PHE C 33 TRP 0.026 0.003 TRP D 51 HIS 0.006 0.002 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.35 ( 8089) covalent geometry : angle 0.81313 / 0.46 (10713) SS BOND : bond 0.00788 / 0.40 ( 4) SS BOND : angle 3.47075 / 2.12 ( 8) hydrogen bonds : bond 0.04854 / 3.83 ( 505) hydrogen bonds : angle 5.77618 / 4.59 ( 1425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 137 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue ALA 142 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue ILE 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue VAL 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue ALA 202 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue TYR 230 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue TYR 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ALA 285 is missing expected H atoms. Skipping. Residue MET 286 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue VAL 289 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue VAL 22 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue TYR 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue TYR 108 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue THR 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue TYR 209 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue SER 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ALA 59 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue TYR 65 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue TYR 103 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue THR 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 166 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue LYS 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue ALA 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 211 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8207 (mm-30) REVERT: B 74 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7614 (tp-100) REVERT: B 99 PHE cc_start: 0.8256 (m-10) cc_final: 0.7998 (m-80) REVERT: C 117 ILE cc_start: 0.8505 (mt) cc_final: 0.8116 (tp) REVERT: D 52 TYR cc_start: 0.7548 (m-80) cc_final: 0.7016 (m-80) outliers start: 14 outliers final: 8 residues processed: 132 average time/residue: 0.2006 time to fit residues: 34.7035 Evaluate side-chains 101 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 125 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN C 120 GLN D 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.141270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.113291 restraints weight = 77592.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.112010 restraints weight = 54475.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.113454 restraints weight = 34026.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.113485 restraints weight = 24844.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.113789 restraints weight = 23636.313| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8093 Z= 0.155 Angle : 0.554 6.252 10721 Z= 0.309 Chirality : 0.043 0.173 844 Planarity : 0.003 0.039 1610 Dihedral : 4.565 28.463 1390 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.19 % Favored : 95.58 % Rotamer: Outliers : 2.96 % Allowed : 10.53 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.16 (0.23), residues: 1313 helix: 2.29 (0.27), residues: 345 sheet: 0.66 (0.25), residues: 410 loop : -0.04 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 254 TYR 0.020 0.001 TYR C 58 PHE 0.013 0.002 PHE C 68 TRP 0.005 0.001 TRP D 51 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8089) covalent geometry : angle 0.55109 / 0.31 (10713) SS BOND : bond 0.00560 / 0.29 ( 4) SS BOND : angle 1.97246 / 1.18 ( 8) hydrogen bonds : bond 0.03865 / 3.02 ( 505) hydrogen bonds : angle 4.78148 / 3.79 ( 1425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 137 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue ALA 142 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue ILE 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue VAL 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue ALA 202 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue TYR 230 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue TYR 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ALA 285 is missing expected H atoms. Skipping. Residue MET 286 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue VAL 289 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue VAL 22 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue TYR 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue TYR 108 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue THR 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue TYR 209 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue SER 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ALA 59 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue TYR 65 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue TYR 103 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue THR 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 166 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue LYS 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue ALA 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 211 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8208 (mm-30) REVERT: B 99 PHE cc_start: 0.8127 (m-10) cc_final: 0.7924 (m-80) REVERT: B 204 HIS cc_start: 0.8329 (m90) cc_final: 0.8070 (m-70) outliers start: 18 outliers final: 14 residues processed: 114 average time/residue: 0.1843 time to fit residues: 28.1096 Evaluate side-chains 106 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN D 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.134938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.108599 restraints weight = 79704.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.107899 restraints weight = 78109.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.109030 restraints weight = 53520.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.109036 restraints weight = 36180.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.109467 restraints weight = 34319.931| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.7792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.135 8093 Z= 0.449 Angle : 0.886 11.195 10721 Z= 0.509 Chirality : 0.051 0.230 844 Planarity : 0.006 0.046 1610 Dihedral : 6.643 36.768 1390 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.91 % Favored : 90.78 % Rotamer: Outliers : 5.10 % Allowed : 12.17 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.64 (0.23), residues: 1313 helix: 1.08 (0.27), residues: 344 sheet: -0.16 (0.25), residues: 414 loop : -1.60 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 225 TYR 0.031 0.003 TYR C 58 PHE 0.036 0.004 PHE C 99 TRP 0.037 0.005 TRP D 107 HIS 0.012 0.002 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00960 / 0.45 ( 8089) covalent geometry : angle 0.88569 / 0.51 (10713) SS BOND : bond 0.00983 / 0.49 ( 4) SS BOND : angle 1.20488 / 0.68 ( 8) hydrogen bonds : bond 0.05061 / 4.01 ( 505) hydrogen bonds : angle 6.16222 / 4.94 ( 1425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 137 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue ALA 142 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue ILE 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue VAL 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue ALA 202 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue TYR 230 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue TYR 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ALA 285 is missing expected H atoms. Skipping. Residue MET 286 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue VAL 289 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue VAL 22 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue TYR 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue TYR 108 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue THR 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue TYR 209 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue SER 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ALA 59 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue TYR 65 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue TYR 103 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue THR 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 166 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue LYS 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue ALA 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 211 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8289 (mm-30) REVERT: B 99 PHE cc_start: 0.8378 (m-10) cc_final: 0.8103 (m-80) REVERT: D 66 ASP cc_start: 0.7959 (m-30) cc_final: 0.7730 (m-30) outliers start: 31 outliers final: 22 residues processed: 108 average time/residue: 0.1916 time to fit residues: 27.0796 Evaluate side-chains 104 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 214 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.134945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.107070 restraints weight = 78776.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.106512 restraints weight = 65911.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.107487 restraints weight = 51780.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.107913 restraints weight = 33956.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.108284 restraints weight = 31135.397| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.8337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 8093 Z= 0.265 Angle : 0.663 12.219 10721 Z= 0.373 Chirality : 0.046 0.272 844 Planarity : 0.004 0.042 1610 Dihedral : 5.667 30.460 1390 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.38 % Favored : 91.47 % Rotamer: Outliers : 4.44 % Allowed : 14.80 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.55 (0.23), residues: 1313 helix: 1.90 (0.28), residues: 329 sheet: -0.20 (0.25), residues: 394 loop : -1.85 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 115 TYR 0.022 0.002 TYR C 58 PHE 0.025 0.002 PHE C 99 TRP 0.016 0.003 TRP D 107 HIS 0.007 0.002 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.26 ( 8089) covalent geometry : angle 0.66260 / 0.37 (10713) SS BOND : bond 0.01124 / 0.55 ( 4) SS BOND : angle 1.18779 / 0.71 ( 8) hydrogen bonds : bond 0.03962 / 3.13 ( 505) hydrogen bonds : angle 5.39671 / 4.33 ( 1425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 137 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue ALA 142 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue ILE 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue VAL 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue ALA 202 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue TYR 230 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue TYR 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ALA 285 is missing expected H atoms. Skipping. Residue MET 286 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue VAL 289 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue VAL 22 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue TYR 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue TYR 108 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue THR 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue TYR 209 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue SER 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ALA 59 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue TYR 65 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue TYR 103 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue THR 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 166 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue LYS 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue ALA 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 211 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8294 (mm-30) REVERT: C 87 LEU cc_start: 0.6917 (tp) cc_final: 0.6642 (tp) REVERT: D 52 TYR cc_start: 0.7792 (m-80) cc_final: 0.7085 (m-80) outliers start: 27 outliers final: 21 residues processed: 100 average time/residue: 0.1666 time to fit residues: 23.1306 Evaluate side-chains 98 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 214 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 110 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 112 optimal weight: 0.1980 chunk 51 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.0020 overall best weight: 2.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** 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 = 0.4275 r_free = 0.4275 target = 0.134785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.107163 restraints weight = 79605.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.106569 restraints weight = 71054.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.107784 restraints weight = 49530.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.108006 restraints weight = 34357.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.108418 restraints weight = 32041.472| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.8703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 8093 Z= 0.236 Angle : 0.638 11.481 10721 Z= 0.356 Chirality : 0.045 0.274 844 Planarity : 0.004 0.042 1610 Dihedral : 5.424 31.422 1390 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.67 % Favored : 90.10 % Rotamer: Outliers : 3.78 % Allowed : 15.46 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.54 (0.23), residues: 1313 helix: 2.15 (0.28), residues: 329 sheet: -0.33 (0.25), residues: 394 loop : -1.90 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 225 TYR 0.020 0.002 TYR C 58 PHE 0.019 0.002 PHE C 99 TRP 0.016 0.002 TRP D 107 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.24 ( 8089) covalent geometry : angle 0.63695 / 0.36 (10713) SS BOND : bond 0.00660 / 0.33 ( 4) SS BOND : angle 1.25440 / 0.73 ( 8) hydrogen bonds : bond 0.03777 / 2.99 ( 505) hydrogen bonds : angle 5.22176 / 4.17 ( 1425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 137 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue ALA 142 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue ILE 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue VAL 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue ALA 202 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue TYR 230 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue TYR 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ALA 285 is missing expected H atoms. Skipping. Residue MET 286 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue VAL 289 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue VAL 22 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue TYR 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue TYR 108 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue THR 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue TYR 209 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue SER 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ALA 59 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue TYR 65 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue TYR 103 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue THR 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 166 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue LYS 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue ALA 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 211 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8286 (mm-30) REVERT: B 130 ASN cc_start: 0.4845 (OUTLIER) cc_final: 0.4570 (p0) REVERT: B 239 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6539 (tt) REVERT: C 87 LEU cc_start: 0.6939 (tp) cc_final: 0.6532 (tp) REVERT: D 52 TYR cc_start: 0.7804 (m-80) cc_final: 0.7458 (m-80) REVERT: D 203 GLU cc_start: 0.8802 (mp0) cc_final: 0.8524 (pm20) outliers start: 23 outliers final: 17 residues processed: 97 average time/residue: 0.1650 time to fit residues: 22.2611 Evaluate side-chains 97 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 13 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.136238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.108323 restraints weight = 78817.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.106395 restraints weight = 71099.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.108375 restraints weight = 42162.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.108297 restraints weight = 30089.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.108517 restraints weight = 28947.724| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.8685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8093 Z= 0.116 Angle : 0.527 8.449 10721 Z= 0.286 Chirality : 0.043 0.193 844 Planarity : 0.003 0.036 1610 Dihedral : 4.634 32.866 1390 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.94 % Favored : 93.91 % Rotamer: Outliers : 2.63 % Allowed : 16.94 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.12 (0.24), residues: 1313 helix: 2.86 (0.29), residues: 329 sheet: -0.03 (0.26), residues: 370 loop : -1.46 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.017 0.001 TYR D 65 PHE 0.043 0.002 PHE B 237 TRP 0.007 0.001 TRP C 54 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 8089) covalent geometry : angle 0.52601 / 0.29 (10713) SS BOND : bond 0.00606 / 0.30 ( 4) SS BOND : angle 1.06620 / 0.65 ( 8) hydrogen bonds : bond 0.03057 / 2.40 ( 505) hydrogen bonds : angle 4.51213 / 3.59 ( 1425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 137 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue ALA 142 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue ILE 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue VAL 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue ALA 202 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue TYR 230 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue TYR 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ALA 285 is missing expected H atoms. Skipping. Residue MET 286 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue VAL 289 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue VAL 22 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue TYR 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue TYR 108 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue THR 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue TYR 209 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue SER 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ALA 59 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue TYR 65 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue TYR 103 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue THR 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 166 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue LYS 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue ALA 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 211 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 239 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6303 (mt) REVERT: C 87 LEU cc_start: 0.6850 (tp) cc_final: 0.6538 (tp) REVERT: D 203 GLU cc_start: 0.8924 (mp0) cc_final: 0.8612 (pm20) outliers start: 16 outliers final: 13 residues processed: 100 average time/residue: 0.1542 time to fit residues: 21.8050 Evaluate side-chains 95 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 51 optimal weight: 50.0000 chunk 33 optimal weight: 30.0000 chunk 52 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 80 optimal weight: 0.3980 chunk 104 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 29 optimal weight: 50.0000 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 50.0000 chunk 19 optimal weight: 10.0000 overall best weight: 5.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 HIS B 157 GLN ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.131596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.105041 restraints weight = 80643.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.104762 restraints weight = 84790.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.105212 restraints weight = 62344.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.105555 restraints weight = 39437.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.105838 restraints weight = 34625.479| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.9685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.142 8093 Z= 0.442 Angle : 0.865 14.059 10721 Z= 0.485 Chirality : 0.051 0.310 844 Planarity : 0.006 0.047 1610 Dihedral : 6.456 45.357 1390 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.88 % Favored : 87.74 % Rotamer: Outliers : 4.93 % Allowed : 16.78 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.20 (0.23), residues: 1313 helix: 1.64 (0.29), residues: 322 sheet: -0.76 (0.26), residues: 384 loop : -2.22 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 225 TYR 0.032 0.003 TYR C 58 PHE 0.042 0.005 PHE C 99 TRP 0.022 0.004 TRP D 107 HIS 0.010 0.002 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.44 ( 8089) covalent geometry : angle 0.86387 / 0.49 (10713) SS BOND : bond 0.01169 / 0.57 ( 4) SS BOND : angle 1.50195 / 0.88 ( 8) hydrogen bonds : bond 0.04869 / 3.91 ( 505) hydrogen bonds : angle 6.02396 / 4.81 ( 1425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 137 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue ALA 142 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue ILE 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue VAL 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue ALA 202 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue TYR 230 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue TYR 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ALA 285 is missing expected H atoms. Skipping. Residue MET 286 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue VAL 289 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue VAL 22 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue TYR 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue TYR 108 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue THR 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue TYR 209 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue SER 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ALA 59 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue TYR 65 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue TYR 103 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue THR 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 166 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue LYS 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue ALA 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 211 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 ASN cc_start: 0.4896 (OUTLIER) cc_final: 0.4603 (p0) REVERT: C 52 MET cc_start: 0.7593 (mmm) cc_final: 0.7231 (mmm) REVERT: C 87 LEU cc_start: 0.7002 (tp) cc_final: 0.6787 (tp) outliers start: 30 outliers final: 26 residues processed: 92 average time/residue: 0.1496 time to fit residues: 19.9284 Evaluate side-chains 94 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 0.0270 chunk 86 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.134021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.104840 restraints weight = 78967.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.103940 restraints weight = 64667.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.105218 restraints weight = 43768.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.105144 restraints weight = 32218.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.105675 restraints weight = 29972.411| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.9580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8093 Z= 0.154 Angle : 0.590 9.478 10721 Z= 0.324 Chirality : 0.044 0.275 844 Planarity : 0.004 0.036 1610 Dihedral : 5.290 41.018 1390 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.00 % Favored : 91.85 % Rotamer: Outliers : 3.12 % Allowed : 19.08 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.56 (0.24), residues: 1313 helix: 2.39 (0.29), residues: 330 sheet: -0.70 (0.26), residues: 404 loop : -1.79 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 102 TYR 0.019 0.002 TYR D 65 PHE 0.037 0.002 PHE B 237 TRP 0.010 0.002 TRP D 51 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8089) covalent geometry : angle 0.58880 / 0.32 (10713) SS BOND : bond 0.00691 / 0.34 ( 4) SS BOND : angle 1.22770 / 0.73 ( 8) hydrogen bonds : bond 0.03346 / 2.64 ( 505) hydrogen bonds : angle 4.99253 / 3.98 ( 1425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 137 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue ALA 142 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue ILE 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue VAL 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue ALA 202 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue TYR 230 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue TYR 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ALA 285 is missing expected H atoms. Skipping. Residue MET 286 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue VAL 289 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue VAL 22 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue TYR 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue TYR 108 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue THR 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue TYR 209 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue SER 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ALA 59 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue TYR 65 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue TYR 103 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue THR 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 166 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue LYS 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue ALA 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 211 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 HIS cc_start: 0.7410 (t-170) cc_final: 0.6710 (t70) REVERT: B 211 MET cc_start: 0.8811 (ttm) cc_final: 0.8506 (tmm) REVERT: D 203 GLU cc_start: 0.8851 (mp0) cc_final: 0.8647 (pm20) outliers start: 19 outliers final: 17 residues processed: 94 average time/residue: 0.1469 time to fit residues: 20.0684 Evaluate side-chains 91 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 0.4980 chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.133903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.104238 restraints weight = 77979.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.103543 restraints weight = 62680.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.104568 restraints weight = 45636.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.104808 restraints weight = 31459.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.105227 restraints weight = 29387.648| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.9670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8093 Z= 0.160 Angle : 0.574 8.023 10721 Z= 0.315 Chirality : 0.043 0.234 844 Planarity : 0.004 0.040 1610 Dihedral : 5.036 38.517 1390 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.68 % Favored : 91.17 % Rotamer: Outliers : 2.63 % Allowed : 19.90 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.32 (0.24), residues: 1313 helix: 2.71 (0.29), residues: 332 sheet: -0.67 (0.26), residues: 404 loop : -1.65 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 115 TYR 0.017 0.002 TYR D 65 PHE 0.035 0.002 PHE B 237 TRP 0.011 0.002 TRP D 51 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 8089) covalent geometry : angle 0.57296 / 0.31 (10713) SS BOND : bond 0.00642 / 0.32 ( 4) SS BOND : angle 1.07856 / 0.64 ( 8) hydrogen bonds : bond 0.03255 / 2.56 ( 505) hydrogen bonds : angle 4.81209 / 3.84 ( 1425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 137 is missing expected H atoms. Skipping. Residue ALA 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue ALA 142 is missing expected H atoms. Skipping. Residue LYS 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue ILE 150 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LEU 161 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue ILE 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue VAL 193 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue ALA 198 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue ALA 202 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue SER 216 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue TYR 230 is missing expected H atoms. Skipping. Residue LEU 231 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ILE 250 is missing expected H atoms. Skipping. Residue THR 251 is missing expected H atoms. Skipping. Residue TYR 252 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue VAL 270 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue SER 273 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue THR 276 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ALA 285 is missing expected H atoms. Skipping. Residue MET 286 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue VAL 289 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue SER 13 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue VAL 22 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue TYR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ALA 44 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue TYR 58 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue TYR 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue THR 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue THR 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue MET 85 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue VAL 97 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue TYR 108 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue THR 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue SER 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue THR 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue VAL 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue ALA 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue VAL 178 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue ALA 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue TYR 209 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue THR 220 is missing expected H atoms. Skipping. Residue LYS 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue SER 38 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ALA 59 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue TYR 65 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 82 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue TYR 103 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue THR 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue ALA 147 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue ALA 150 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue TYR 160 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 166 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue LYS 169 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue ALA 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 196 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 211 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Residue LYS 224 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 HIS cc_start: 0.7404 (t-170) cc_final: 0.6695 (t70) REVERT: B 211 MET cc_start: 0.8769 (ttm) cc_final: 0.8496 (tmm) outliers start: 16 outliers final: 16 residues processed: 89 average time/residue: 0.1481 time to fit residues: 18.8483 Evaluate side-chains 87 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.134252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.105139 restraints weight = 77658.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.104344 restraints weight = 66206.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.105428 restraints weight = 46905.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.105622 restraints weight = 31159.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.106018 restraints weight = 29104.795| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.9742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8093 Z= 0.144 Angle : 0.555 7.687 10721 Z= 0.304 Chirality : 0.043 0.217 844 Planarity : 0.004 0.041 1610 Dihedral : 4.865 36.294 1390 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.53 % Favored : 91.32 % Rotamer: Outliers : 3.12 % Allowed : 19.24 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.14 (0.24), residues: 1313 helix: 2.89 (0.29), residues: 333 sheet: -0.56 (0.26), residues: 392 loop : -1.56 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 115 TYR 0.014 0.002 TYR C 58 PHE 0.034 0.002 PHE B 237 TRP 0.010 0.002 TRP D 51 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8089) covalent geometry : angle 0.55467 / 0.30 (10713) SS BOND : bond 0.00587 / 0.29 ( 4) SS BOND : angle 1.01092 / 0.61 ( 8) hydrogen bonds : bond 0.03105 / 2.44 ( 505) hydrogen bonds : angle 4.64362 / 3.70 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.45 seconds wall clock time: 41 minutes 56.63 seconds (2516.63 seconds total)