Starting phenix.real_space_refine on Wed Aug 5 01:40:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z7t_73880/08_2026/9z7t_73880_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z7t_73880/08_2026/9z7t_73880.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9z7t_73880/08_2026/9z7t_73880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z7t_73880/08_2026/9z7t_73880.map" model { file = "/net/cci-nas-00/data/ceres_data/9z7t_73880/08_2026/9z7t_73880_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z7t_73880/08_2026/9z7t_73880_trim.cif" } 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= 0.031 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: 7 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 15 5.16 5 C 2688 2.51 5 N 693 2.21 5 O 725 1.98 5 H 3663 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7788 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 3839 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 288} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 8, 'ASN:plan1': 3, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 3916 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 287} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 2, 'ASP:plan': 2, 'GLU:plan': 9, 'PHE:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 1.60, per 1000 atoms: 0.21 Number of scatterers: 7788 At special positions: 0 Unit cell: (66.5721, 103.557, 67.6288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 15 16.00 P 3 15.00 Mg 1 11.99 O 725 8.00 N 693 7.00 C 2688 6.00 H 3663 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 311.5 milliseconds 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1074 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 4 through 42 removed outlier: 3.502A pdb=" N ILE A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 41 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.755A pdb=" N ALA A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.683A pdb=" N VAL A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 104 removed outlier: 3.581A pdb=" N SER A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.715A pdb=" N HIS A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 148 through 166 Processing helix chain 'A' and resid 178 through 209 removed outlier: 3.605A pdb=" N ILE A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 243 removed outlier: 4.147A pdb=" N TRP A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 268 Processing helix chain 'A' and resid 275 through 299 removed outlier: 3.644A pdb=" N PHE A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 43 removed outlier: 3.648A pdb=" N ASP B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE B 10 " --> pdb=" O GLY B 6 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.535A pdb=" N LEU B 54 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 80 removed outlier: 3.859A pdb=" N TRP B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 90 through 104 removed outlier: 3.890A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 128 removed outlier: 3.563A pdb=" N LYS B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 4.041A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 174 removed outlier: 3.539A pdb=" N PHE B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 178 through 209 removed outlier: 3.791A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 243 removed outlier: 4.147A pdb=" N TRP B 219 " --> pdb=" O HIS B 215 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.530A pdb=" N MET B 274 " --> pdb=" O TRP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 299 removed outlier: 3.667A pdb=" N PHE B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3654 1.03 - 1.23: 9 1.23 - 1.42: 1757 1.42 - 1.61: 2437 1.61 - 1.81: 23 Bond restraints: 7880 Sorted by residual: bond pdb=" O5' ATP A 401 " pdb=" PA ATP A 401 " ideal model delta sigma weight residual 1.579 1.655 -0.076 1.10e-02 8.26e+03 4.72e+01 bond pdb=" C1' ATP A 401 " pdb=" C2' ATP A 401 " ideal model delta sigma weight residual 1.531 1.599 -0.068 1.20e-02 6.94e+03 3.25e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.336 0.052 1.00e-02 1.00e+04 2.70e+01 bond pdb=" C5 ATP A 401 " pdb=" N7 ATP A 401 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 2.06e+01 bond pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 1.374 1.334 0.040 1.00e-02 1.00e+04 1.62e+01 ... (remaining 7875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.03: 14079 6.03 - 12.06: 8 12.06 - 18.09: 2 18.09 - 24.11: 2 24.11 - 30.14: 9 Bond angle restraints: 14100 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 123.24 16.63 1.00e+00 1.00e+00 2.76e+02 angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 122.55 14.28 1.00e+00 1.00e+00 2.04e+02 angle pdb=" SD MET A 66 " pdb=" CE MET A 66 " pdb=" HE2 MET A 66 " ideal model delta sigma weight residual 109.00 78.86 30.14 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CB LYS A 31 " pdb=" CG LYS A 31 " pdb=" HG3 LYS A 31 " ideal model delta sigma weight residual 109.00 79.65 29.35 3.00e+00 1.11e-01 9.57e+01 angle pdb=" SD MET A 66 " pdb=" CE MET A 66 " pdb=" HE1 MET A 66 " ideal model delta sigma weight residual 109.00 79.78 29.22 3.00e+00 1.11e-01 9.48e+01 ... (remaining 14095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3358 17.70 - 35.39: 304 35.39 - 53.09: 122 53.09 - 70.78: 47 70.78 - 88.48: 2 Dihedral angle restraints: 3833 sinusoidal: 1865 harmonic: 1968 Sorted by residual: dihedral pdb=" N LEU A 118 " pdb=" CA LEU A 118 " pdb=" CB LEU A 118 " pdb=" CG LEU A 118 " ideal model delta sinusoidal sigma weight residual -60.00 -110.44 50.44 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" N MET B 126 " pdb=" CA MET B 126 " pdb=" CB MET B 126 " pdb=" CG MET B 126 " ideal model delta sinusoidal sigma weight residual -60.00 -107.70 47.70 3 1.50e+01 4.44e-03 8.53e+00 dihedral pdb=" N ASN A 237 " pdb=" CA ASN A 237 " pdb=" CB ASN A 237 " pdb=" CG ASN A 237 " ideal model delta sinusoidal sigma weight residual -60.00 -107.29 47.29 3 1.50e+01 4.44e-03 8.47e+00 ... (remaining 3830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 509 0.033 - 0.067: 134 0.067 - 0.100: 56 0.100 - 0.133: 8 0.133 - 0.167: 1 Chirality restraints: 708 Sorted by residual: chirality pdb=" C1' ATP A 401 " pdb=" C2' ATP A 401 " pdb=" N9 ATP A 401 " pdb=" O4' ATP A 401 " both_signs ideal model delta sigma weight residual False 2.41 2.58 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CB ILE A 160 " pdb=" CA ILE A 160 " pdb=" CG1 ILE A 160 " pdb=" CG2 ILE A 160 " both_signs ideal model delta sigma weight residual False 2.64 2.77 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA ILE B 136 " pdb=" N ILE B 136 " pdb=" C ILE B 136 " pdb=" CB ILE B 136 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 705 not shown) Planarity restraints: 1281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 249 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO B 250 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 250 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 250 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 274 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO B 275 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 275 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 275 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 249 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO A 250 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " 0.024 5.00e-02 4.00e+02 ... (remaining 1278 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 877 2.24 - 2.83: 16126 2.83 - 3.42: 20025 3.42 - 4.01: 24421 4.01 - 4.60: 37740 Nonbonded interactions: 99189 Sorted by model distance: nonbonded pdb=" HB2 LYS A 31 " pdb=" HG3 LYS A 31 " model vdw 1.653 1.952 nonbonded pdb=" HB3 LYS A 31 " pdb=" HG2 LYS A 31 " model vdw 1.712 1.952 nonbonded pdb=" HG2 LYS A 31 " pdb=" HD2 LYS A 31 " model vdw 1.799 1.952 nonbonded pdb=" HG SER B 123 " pdb=" HE1 TYR B 253 " model vdw 1.861 2.100 nonbonded pdb=" O2G ATP A 401 " pdb="MG MG A 402 " model vdw 1.864 2.050 ... (remaining 99184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 or (resid 5 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 6 through 7 or (resid 8 through 9 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 10 through 11 or (resid 12 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 13 or (resid 14 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 15 through 17 or (r \ esid 18 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 19 through 21 or (resid 22 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 23 through 28 or (resid 29 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or (re \ sid 30 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name H or name HA )) or resid 31 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE or name NZ or name H or name HA )) or resid 34 through 53 or (resid 54 throug \ h 56 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 57 through 63 or (resid 64 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 65 through 69 or (resid 70 through \ 71 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 72 through 73 or (resid 74 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 75 through 78 or (resid 79 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ or name H or name HA )) or (resid 80 and (na \ me N or name CA or name C or name O or name CB )) or (resid 81 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD )) or (resid 82 throu \ gh 86 and (name N or name CA or name C or name O or name CB )) or (resid 87 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or (r \ esid 88 and (name N or name CA or name C or name O or name CB )) or resid 89 or \ (resid 90 through 91 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 92 through 101 or (resid 102 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 103 through 105 \ or (resid 106 through 107 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 108 through 139 or (resid 140 and (name N or na \ me CA or name C or name O or name CB or name CG or name OD1 or name ND2 or name \ H or name HA )) or (resid 141 through 144 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 145 through 168 or (resid 169 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 170 through 174 or (resid 175 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name OE1 or name NE2 or name H or name HA )) \ or resid 176 or (resid 177 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or (resid 178 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1)) or resid 179 through 195 or ( \ resid 196 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 197 through 198 or (resid 199 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 200 or (resid 201 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 02 or (resid 203 through 207 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 208 through 211 or (resid 212 through 213 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 214 or (resid 215 and (name N or name CA or name C or name O or name CB or \ name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA )) \ or resid 216 through 218 or (resid 219 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 or name \ CE3 or name CZ2 or name CZ3 or name CH2 or name H or name HA )) or resid 220 thr \ ough 245 or (resid 246 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 247 through 300)) selection = (chain 'B' and ((resid 4 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 5 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 33 through 34 or (resid \ 35 through 36 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 37 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or (resid 42 and (name N or name C \ A or name C or name O or name H )) or (resid 43 through 46 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or (resid 47 and (name \ N or name CA or name C or name O or name H )) or (resid 48 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or (resid 49 through 50 \ and (name N or name CA or name C or name O or name H )) or (resid 51 through 52 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 53 through 92 or (resid 93 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 94 through 103 or (resid 104 and (name \ N or name CA or name C or name O or name CB )) or (resid 105 through 107 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or (resi \ d 108 and (name N or name CA or name C or name O or name CB or name H or name HA \ or name HB2 or name HB3)) or (resid 109 through 110 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 111 through 144 or ( \ resid 145 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name CE or name NZ or name H or name HA )) or (resid 146 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 147 thr \ ough 152 or (resid 153 through 154 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 155 through 156 or (resid 157 through \ 159 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 160 through 162 or (resid 163 through 165 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 166 or (resid 167 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 168 through 171 or (resid 172 through 173 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 174 through 206 or (resid \ 207 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 208 through 213 or (resid 214 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name H or name HA )) or resid 215 through 219 or (resid 220 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 221 or \ (resid 222 through 223 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 224 or (resid 225 through 226 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 227 or (resid \ 228 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 229 or (resid 230 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 231 through 239 or (resid 240 through 246 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 247 through 266 or (resid 267 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 268 through 269 or (resid 270 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 271 through 273 or (resid 274 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 275 through 276 or (resid 277 through 278 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 279 through 299 or (resid 300 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )))) } 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.090 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 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 : 0.004 0.076 4218 Z= 0.260 Angle : 0.696 16.626 5782 Z= 0.479 Chirality : 0.036 0.167 708 Planarity : 0.005 0.053 715 Dihedral : 15.522 88.480 1332 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 33.05 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.68 (0.36), residues: 591 helix: 3.28 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -0.24 (0.56), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 45 TYR 0.009 0.001 TYR B 253 PHE 0.007 0.001 PHE A 256 TRP 0.015 0.001 TRP A 57 HIS 0.007 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.26 ( 4217) covalent geometry : angle 0.69595 / 0.48 ( 5782) hydrogen bonds : bond 0.12548 / 8.68 ( 370) hydrogen bonds : angle 6.21994 / 4.75 ( 1104) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue MET 274 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ALA 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8268 (mmt) cc_final: 0.7841 (mmt) REVERT: A 19 SER cc_start: 0.9147 (m) cc_final: 0.8839 (t) REVERT: A 269 LYS cc_start: 0.8256 (mttt) cc_final: 0.7965 (mmtt) REVERT: B 37 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7516 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0680 time to fit residues: 11.0602 Evaluate side-chains 114 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN B 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145678 restraints weight = 19128.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151273 restraints weight = 8543.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.154661 restraints weight = 4652.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.156863 restraints weight = 2940.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.158366 restraints weight = 2055.226| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4218 Z= 0.140 Angle : 0.543 10.735 5782 Z= 0.302 Chirality : 0.035 0.121 708 Planarity : 0.005 0.042 715 Dihedral : 7.933 89.077 653 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.52 % Allowed : 29.41 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.59 (0.35), residues: 591 helix: 3.23 (0.23), residues: 436 sheet: None (None), residues: 0 loop : -0.28 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.014 0.001 TYR B 11 PHE 0.008 0.001 PHE B 28 TRP 0.008 0.001 TRP A 57 HIS 0.006 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 4217) covalent geometry : angle 0.54274 / 0.30 ( 5782) hydrogen bonds : bond 0.04622 / 3.22 ( 370) hydrogen bonds : angle 4.42023 / 3.26 ( 1104) Misc. bond : bond 0.00086 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue MET 274 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ALA 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8172 (mmt) cc_final: 0.7801 (mmt) REVERT: A 19 SER cc_start: 0.9176 (m) cc_final: 0.8866 (t) REVERT: A 269 LYS cc_start: 0.8350 (mttt) cc_final: 0.8122 (mmtm) REVERT: B 11 TYR cc_start: 0.7170 (t80) cc_final: 0.6847 (t80) REVERT: B 32 LYS cc_start: 0.8498 (tptp) cc_final: 0.8008 (tptt) REVERT: B 37 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7567 (mmm160) outliers start: 9 outliers final: 7 residues processed: 122 average time/residue: 0.0823 time to fit residues: 14.1928 Evaluate side-chains 120 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 284 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.163796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147004 restraints weight = 18726.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151932 restraints weight = 8812.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155084 restraints weight = 4991.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.157094 restraints weight = 3187.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158400 restraints weight = 2245.538| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4218 Z= 0.163 Angle : 0.538 10.738 5782 Z= 0.304 Chirality : 0.035 0.121 708 Planarity : 0.004 0.042 715 Dihedral : 7.256 87.135 653 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.92 % Allowed : 27.17 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.51 (0.35), residues: 591 helix: 3.21 (0.23), residues: 436 sheet: None (None), residues: 0 loop : -0.43 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 214 TYR 0.008 0.001 TYR B 11 PHE 0.010 0.001 PHE A 74 TRP 0.014 0.001 TRP A 57 HIS 0.008 0.002 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 4217) covalent geometry : angle 0.53837 / 0.30 ( 5782) hydrogen bonds : bond 0.04504 / 3.14 ( 370) hydrogen bonds : angle 4.35812 / 3.23 ( 1104) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue MET 274 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ALA 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.9241 (m) cc_final: 0.8939 (t) REVERT: A 269 LYS cc_start: 0.8461 (mttt) cc_final: 0.8142 (mmtm) REVERT: B 77 TYR cc_start: 0.6797 (OUTLIER) cc_final: 0.6338 (m-10) outliers start: 14 outliers final: 11 residues processed: 114 average time/residue: 0.0783 time to fit residues: 12.6118 Evaluate side-chains 118 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 284 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146603 restraints weight = 19049.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151714 restraints weight = 8983.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154884 restraints weight = 5043.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156922 restraints weight = 3209.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.158282 restraints weight = 2251.904| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4218 Z= 0.147 Angle : 0.527 10.683 5782 Z= 0.296 Chirality : 0.034 0.120 708 Planarity : 0.005 0.050 715 Dihedral : 6.970 79.239 653 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.92 % Allowed : 26.33 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.48 (0.35), residues: 591 helix: 3.09 (0.23), residues: 442 sheet: None (None), residues: 0 loop : -0.23 (0.56), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 37 TYR 0.014 0.001 TYR B 11 PHE 0.009 0.001 PHE A 74 TRP 0.010 0.001 TRP A 57 HIS 0.006 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 ( 4217) covalent geometry : angle 0.52738 / 0.30 ( 5782) hydrogen bonds : bond 0.04235 / 2.96 ( 370) hydrogen bonds : angle 4.21401 / 3.13 ( 1104) Misc. bond : bond 0.00129 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue MET 274 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ALA 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.9256 (m) cc_final: 0.8940 (t) REVERT: A 269 LYS cc_start: 0.8477 (mttt) cc_final: 0.8183 (mmtm) REVERT: B 37 ARG cc_start: 0.7795 (mmm160) cc_final: 0.7378 (ttp-170) REVERT: B 77 TYR cc_start: 0.6798 (OUTLIER) cc_final: 0.6316 (m-10) outliers start: 14 outliers final: 10 residues processed: 118 average time/residue: 0.0790 time to fit residues: 13.2941 Evaluate side-chains 117 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 284 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.0370 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.160458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142750 restraints weight = 18971.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.148150 restraints weight = 8311.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151502 restraints weight = 4488.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153583 restraints weight = 2791.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.155016 restraints weight = 1939.668| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4218 Z= 0.131 Angle : 0.518 10.740 5782 Z= 0.287 Chirality : 0.034 0.119 708 Planarity : 0.004 0.046 715 Dihedral : 6.843 78.171 653 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.36 % Allowed : 27.73 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.57 (0.35), residues: 591 helix: 3.15 (0.23), residues: 442 sheet: None (None), residues: 0 loop : -0.19 (0.56), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.010 0.001 TYR B 11 PHE 0.009 0.001 PHE A 74 TRP 0.016 0.001 TRP A 57 HIS 0.006 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 4217) covalent geometry : angle 0.51765 / 0.29 ( 5782) hydrogen bonds : bond 0.04106 / 2.88 ( 370) hydrogen bonds : angle 4.13418 / 3.07 ( 1104) Misc. bond : bond 0.00109 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue MET 274 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ALA 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.9249 (m) cc_final: 0.8937 (t) REVERT: A 269 LYS cc_start: 0.8528 (mttt) cc_final: 0.8243 (mmtt) REVERT: B 37 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7427 (ttp-170) REVERT: B 77 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6339 (m-10) outliers start: 12 outliers final: 10 residues processed: 116 average time/residue: 0.0877 time to fit residues: 14.2517 Evaluate side-chains 117 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 284 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141977 restraints weight = 18867.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147370 restraints weight = 8270.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150652 restraints weight = 4462.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152756 restraints weight = 2786.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.154155 restraints weight = 1928.802| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4218 Z= 0.142 Angle : 0.534 10.816 5782 Z= 0.295 Chirality : 0.034 0.120 708 Planarity : 0.004 0.042 715 Dihedral : 6.735 75.767 653 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.92 % Allowed : 27.17 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.54 (0.35), residues: 591 helix: 3.13 (0.23), residues: 442 sheet: None (None), residues: 0 loop : -0.22 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.010 0.001 TYR B 11 PHE 0.010 0.001 PHE A 74 TRP 0.013 0.001 TRP A 57 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 4217) covalent geometry : angle 0.53414 / 0.30 ( 5782) hydrogen bonds : bond 0.04065 / 2.85 ( 370) hydrogen bonds : angle 4.11621 / 3.06 ( 1104) Misc. bond : bond 0.00105 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue MET 274 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ALA 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.9303 (m) cc_final: 0.8997 (t) REVERT: A 269 LYS cc_start: 0.8565 (mttt) cc_final: 0.8275 (mmtt) REVERT: B 37 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7450 (ttp-170) REVERT: B 77 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6355 (m-10) outliers start: 14 outliers final: 11 residues processed: 110 average time/residue: 0.0708 time to fit residues: 11.0892 Evaluate side-chains 115 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 284 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142301 restraints weight = 18943.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147676 restraints weight = 8336.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150988 restraints weight = 4513.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.152909 restraints weight = 2812.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154444 restraints weight = 2002.806| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4218 Z= 0.135 Angle : 0.526 10.802 5782 Z= 0.290 Chirality : 0.034 0.120 708 Planarity : 0.004 0.041 715 Dihedral : 6.644 74.201 653 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.20 % Allowed : 26.61 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.55 (0.35), residues: 591 helix: 3.06 (0.24), residues: 446 sheet: None (None), residues: 0 loop : -0.03 (0.58), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.010 0.001 TYR B 11 PHE 0.010 0.001 PHE A 74 TRP 0.012 0.001 TRP A 57 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 4217) covalent geometry : angle 0.52571 / 0.29 ( 5782) hydrogen bonds : bond 0.04013 / 2.82 ( 370) hydrogen bonds : angle 4.07697 / 3.03 ( 1104) Misc. bond : bond 0.00111 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue MET 274 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ALA 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.9305 (m) cc_final: 0.8993 (t) REVERT: A 199 LEU cc_start: 0.8092 (tp) cc_final: 0.7634 (tp) REVERT: A 269 LYS cc_start: 0.8575 (mttt) cc_final: 0.8286 (mmtt) REVERT: B 77 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6398 (m-10) outliers start: 15 outliers final: 14 residues processed: 111 average time/residue: 0.0812 time to fit residues: 12.9383 Evaluate side-chains 120 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 284 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.161746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143976 restraints weight = 19498.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.149433 restraints weight = 8719.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152904 restraints weight = 4801.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155004 restraints weight = 3010.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156187 restraints weight = 2091.483| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4218 Z= 0.132 Angle : 0.525 10.812 5782 Z= 0.289 Chirality : 0.034 0.120 708 Planarity : 0.005 0.065 715 Dihedral : 6.579 73.518 653 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.64 % Allowed : 26.89 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.58 (0.35), residues: 591 helix: 3.08 (0.24), residues: 446 sheet: None (None), residues: 0 loop : -0.00 (0.58), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 37 TYR 0.010 0.001 TYR B 11 PHE 0.010 0.001 PHE A 74 TRP 0.014 0.001 TRP B 59 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 4217) covalent geometry : angle 0.52493 / 0.29 ( 5782) hydrogen bonds : bond 0.03962 / 2.79 ( 370) hydrogen bonds : angle 4.04611 / 3.00 ( 1104) Misc. bond : bond 0.00114 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue MET 274 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ALA 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.9306 (m) cc_final: 0.8992 (t) REVERT: A 199 LEU cc_start: 0.8084 (tp) cc_final: 0.7622 (tp) REVERT: A 269 LYS cc_start: 0.8585 (mttt) cc_final: 0.8295 (mmtt) REVERT: B 37 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7585 (mmm-85) REVERT: B 77 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6552 (m-10) outliers start: 13 outliers final: 12 residues processed: 114 average time/residue: 0.0905 time to fit residues: 14.4763 Evaluate side-chains 119 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 284 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.161950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144245 restraints weight = 19522.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.149634 restraints weight = 8787.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.153070 restraints weight = 4875.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155212 restraints weight = 3071.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.156402 restraints weight = 2127.630| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4218 Z= 0.149 Angle : 0.537 10.841 5782 Z= 0.299 Chirality : 0.035 0.121 708 Planarity : 0.005 0.052 715 Dihedral : 6.550 74.139 653 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.48 % Allowed : 26.33 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.55 (0.35), residues: 591 helix: 3.07 (0.24), residues: 444 sheet: None (None), residues: 0 loop : -0.02 (0.57), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 37 TYR 0.010 0.001 TYR B 11 PHE 0.010 0.001 PHE A 74 TRP 0.019 0.002 TRP A 57 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 4217) covalent geometry : angle 0.53683 / 0.30 ( 5782) hydrogen bonds : bond 0.04009 / 2.82 ( 370) hydrogen bonds : angle 4.07801 / 3.03 ( 1104) Misc. bond : bond 0.00107 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue MET 274 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ALA 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.9340 (m) cc_final: 0.9035 (t) REVERT: A 199 LEU cc_start: 0.8083 (tp) cc_final: 0.7669 (tp) REVERT: A 269 LYS cc_start: 0.8556 (mttt) cc_final: 0.8269 (mmtt) REVERT: B 37 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7591 (mmm-85) REVERT: B 77 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6611 (m-80) outliers start: 16 outliers final: 14 residues processed: 114 average time/residue: 0.0857 time to fit residues: 13.7108 Evaluate side-chains 119 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 284 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.0040 chunk 30 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145647 restraints weight = 19374.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151166 restraints weight = 8658.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154670 restraints weight = 4744.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156794 restraints weight = 2954.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.158240 restraints weight = 2025.098| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4218 Z= 0.119 Angle : 0.517 10.810 5782 Z= 0.284 Chirality : 0.034 0.119 708 Planarity : 0.004 0.048 715 Dihedral : 6.539 77.104 653 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.36 % Allowed : 26.89 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.73 (0.35), residues: 591 helix: 3.17 (0.24), residues: 445 sheet: None (None), residues: 0 loop : 0.16 (0.58), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 37 TYR 0.010 0.001 TYR B 11 PHE 0.009 0.001 PHE A 74 TRP 0.022 0.001 TRP A 57 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 4217) covalent geometry : angle 0.51744 / 0.28 ( 5782) hydrogen bonds : bond 0.03879 / 2.74 ( 370) hydrogen bonds : angle 3.98668 / 2.95 ( 1104) Misc. bond : bond 0.00101 / 0.06 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 7 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue ALA 52 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue SER 230 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue MET 274 is missing expected H atoms. Skipping. Residue LYS 300 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue MET 18 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Residue ALA 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.9298 (m) cc_final: 0.8984 (t) REVERT: A 199 LEU cc_start: 0.8053 (tp) cc_final: 0.7599 (tp) REVERT: A 269 LYS cc_start: 0.8525 (mttt) cc_final: 0.8250 (mmtm) REVERT: B 37 ARG cc_start: 0.7826 (mmm160) cc_final: 0.7498 (mmm-85) REVERT: B 77 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.6542 (m-10) outliers start: 12 outliers final: 11 residues processed: 110 average time/residue: 0.0831 time to fit residues: 13.0035 Evaluate side-chains 116 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 284 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.162615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145134 restraints weight = 19359.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.150539 restraints weight = 8663.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154034 restraints weight = 4776.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.156098 restraints weight = 2970.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157540 restraints weight = 2052.146| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4218 Z= 0.141 Angle : 0.529 10.884 5782 Z= 0.294 Chirality : 0.035 0.120 708 Planarity : 0.004 0.043 715 Dihedral : 6.538 77.178 653 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.64 % Allowed : 26.61 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.64 (0.35), residues: 591 helix: 3.11 (0.24), residues: 445 sheet: None (None), residues: 0 loop : 0.10 (0.58), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 37 TYR 0.010 0.001 TYR B 11 PHE 0.010 0.001 PHE A 74 TRP 0.020 0.002 TRP A 57 HIS 0.006 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 4217) covalent geometry : angle 0.52855 / 0.29 ( 5782) hydrogen bonds : bond 0.03917 / 2.76 ( 370) hydrogen bonds : angle 4.01602 / 2.97 ( 1104) Misc. bond : bond 0.00093 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1375.83 seconds wall clock time: 24 minutes 6.18 seconds (1446.18 seconds total)