Starting phenix.real_space_refine on Wed Aug 5 07:11:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z6n_73843/08_2026/9z6n_73843.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z6n_73843/08_2026/9z6n_73843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z6n_73843/08_2026/9z6n_73843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z6n_73843/08_2026/9z6n_73843.map" model { file = "/net/cci-nas-00/data/ceres_data/9z6n_73843/08_2026/9z6n_73843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z6n_73843/08_2026/9z6n_73843.cif" } resolution = 3.7 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 19 5.16 5 C 2867 2.51 5 N 707 2.21 5 O 756 1.98 5 H 4284 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s 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: 8633 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4308 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4325 Classifications: {'peptide': 306} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 296} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 7, 'PHE:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Time building chain proxies: 1.33, per 1000 atoms: 0.15 Number of scatterers: 8633 At special positions: 0 Unit cell: (71.61, 99.51, 70.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 O 756 8.00 N 707 7.00 C 2867 6.00 H 4284 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=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 336.3 milliseconds 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1094 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 84.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 4 through 41 removed outlier: 3.720A pdb=" N GLY A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 41 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 55 removed outlier: 3.937A pdb=" N LYS A 55 " --> pdb=" O ALA A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 55' Processing helix chain 'A' and resid 56 through 77 removed outlier: 3.626A pdb=" N TRP A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.713A pdb=" N GLY A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 removed outlier: 3.582A pdb=" N MET A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 167 removed outlier: 4.173A pdb=" N ILE A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 209 removed outlier: 4.214A pdb=" N ILE A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 Processing helix chain 'A' and resid 215 through 243 removed outlier: 4.304A pdb=" N TRP A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 269 Processing helix chain 'A' and resid 275 through 299 removed outlier: 3.682A pdb=" N PHE A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 43 removed outlier: 4.274A pdb=" N LYS B 32 " --> pdb=" O PHE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 56 through 80 removed outlier: 4.010A pdb=" N TRP B 60 " --> pdb=" O GLU B 56 " (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 103 removed outlier: 3.787A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 128 Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 148 through 168 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.822A pdb=" N ARG B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 209 Processing helix chain 'B' and resid 216 through 243 removed outlier: 4.113A pdb=" N ILE B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 4.232A 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 275 through 299 removed outlier: 3.506A pdb=" N PHE B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1122 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: 1.69 Time building geometry restraints manager: 1.01 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: 4274 1.03 - 1.22: 10 1.22 - 1.42: 1825 1.42 - 1.61: 2592 1.61 - 1.81: 28 Bond restraints: 8729 Sorted by residual: bond pdb=" C THR A 86 " pdb=" O THR A 86 " ideal model delta sigma weight residual 1.244 1.237 0.006 9.80e-03 1.04e+04 4.29e-01 bond pdb=" C ILE B 24 " pdb=" O ILE B 24 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.13e-02 7.83e+03 3.84e-01 bond pdb=" CA PRO A 171 " pdb=" C PRO A 171 " ideal model delta sigma weight residual 1.528 1.520 0.007 1.20e-02 6.94e+03 3.78e-01 bond pdb=" CG PRO A 250 " pdb=" CD PRO A 250 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.48e-01 bond pdb=" C THR A 249 " pdb=" N PRO A 250 " ideal model delta sigma weight residual 1.336 1.343 -0.007 1.20e-02 6.94e+03 3.36e-01 ... (remaining 8724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 14985 1.11 - 2.22: 758 2.22 - 3.33: 23 3.33 - 4.44: 13 4.44 - 5.55: 1 Bond angle restraints: 15780 Sorted by residual: angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.71e+00 angle pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " pdb=" NH2 ARG A 40 " ideal model delta sigma weight residual 119.20 121.44 -2.24 9.00e-01 1.23e+00 6.19e+00 angle pdb=" NE ARG A 37 " pdb=" CZ ARG A 37 " pdb=" NH2 ARG A 37 " ideal model delta sigma weight residual 119.20 121.44 -2.24 9.00e-01 1.23e+00 6.17e+00 angle pdb=" C SER B 27 " pdb=" N PHE B 28 " pdb=" CA PHE B 28 " ideal model delta sigma weight residual 122.56 118.67 3.89 1.72e+00 3.38e-01 5.12e+00 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH1 ARG A 5 " ideal model delta sigma weight residual 121.50 119.26 2.24 1.00e+00 1.00e+00 5.03e+00 ... (remaining 15775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 3552 11.99 - 23.98: 377 23.98 - 35.98: 80 35.98 - 47.97: 40 47.97 - 59.96: 93 Dihedral angle restraints: 4142 sinusoidal: 2103 harmonic: 2039 Sorted by residual: dihedral pdb=" CA PHE B 28 " pdb=" C PHE B 28 " pdb=" N ILE B 29 " pdb=" CA ILE B 29 " ideal model delta harmonic sigma weight residual 180.00 159.88 20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU B 157 " pdb=" CB LEU B 157 " pdb=" CG LEU B 157 " pdb=" CD1 LEU B 157 " ideal model delta sinusoidal sigma weight residual 180.00 138.00 42.00 3 1.50e+01 4.44e-03 7.53e+00 dihedral pdb=" N LEU A 261 " pdb=" CA LEU A 261 " pdb=" CB LEU A 261 " pdb=" CG LEU A 261 " ideal model delta sinusoidal sigma weight residual -60.00 -100.66 40.66 3 1.50e+01 4.44e-03 7.25e+00 ... (remaining 4139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 517 0.027 - 0.055: 138 0.055 - 0.082: 77 0.082 - 0.109: 15 0.109 - 0.136: 4 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA ILE B 178 " pdb=" N ILE B 178 " pdb=" C ILE B 178 " pdb=" CB ILE B 178 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA PHE B 28 " pdb=" N PHE B 28 " pdb=" C PHE B 28 " pdb=" CB PHE B 28 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-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 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 748 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 155 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C ALA A 155 " 0.026 2.00e-02 2.50e+03 pdb=" O ALA A 155 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 156 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 86 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 87 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 28 " 0.010 2.00e-02 2.50e+03 6.33e-03 1.20e+00 pdb=" CG PHE B 28 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 28 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 28 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 28 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 28 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 28 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE B 28 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE B 28 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 28 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 28 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 28 " -0.000 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 336 2.17 - 2.78: 16637 2.78 - 3.38: 24357 3.38 - 3.99: 27979 3.99 - 4.60: 45087 Nonbonded interactions: 114396 Sorted by model distance: nonbonded pdb=" O ILE B 24 " pdb=" HG SER B 27 " model vdw 1.560 2.450 nonbonded pdb=" OE1 GLU A 270 " pdb=" H GLU A 270 " model vdw 1.626 2.450 nonbonded pdb=" HZ3 LYS B 32 " pdb=" O LEU B 240 " model vdw 1.632 2.450 nonbonded pdb=" O ALA B 82 " pdb=" HG1 THR B 86 " model vdw 1.703 2.450 nonbonded pdb=" O MET A 18 " pdb=" HG SER A 21 " model vdw 1.720 2.450 ... (remaining 114391 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 28 or (resid 29 through 30 \ and (name N or name CA or name C or name O or name CB 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 H or name HA )) or resid 34 through 37 or (resid 38 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 39 th \ rough 54 or (resid 55 through 56 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 57 through 69 or (resid 70 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 71 thr \ ough 78 or (resid 79 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 80 through 83 or (resid 84 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 85 through 87 or ( \ resid 88 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 89 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 131 \ or (resid 132 through 145 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 146 through 150 or (resid 151 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 152 throug \ h 168 or (resid 169 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 170 through 172 or (resid 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 or (resid 17 \ 5 and (name N or name CA or name C or name O or 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 (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 178 through 214 or (resid 215 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 216 through 218 or (resid 219 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 220 th \ rough 300 or (resid 301 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 302)) 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 CG or name CD or name CE or name NZ or name H or \ name HA )) or resid 33 through 42 or (resid 43 through 45 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 46 through 47 o \ r (resid 48 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 49 through 55 or (resid 56 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 57 through 103 or (resid 10 \ 4 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 105 through 106 or (resid 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 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA or name HB2 or name HB3)) or (resi \ d 109 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 110 through 144 or (resid 145 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 146 through 166 or (resid 167 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 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 203 or (resi \ d 204 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 213 or (resid 214 through 215 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 216 th \ rough 222 or (resid 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 through 242 or (resid 243 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 244 through \ 277 or (resid 278 and (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 through 301 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 302)) } 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: 1.490 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: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.620 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.002 0.020 4445 Z= 0.111 Angle : 0.425 5.547 6071 Z= 0.251 Chirality : 0.034 0.136 751 Planarity : 0.003 0.033 743 Dihedral : 10.626 58.438 1448 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.35 (0.36), residues: 601 helix: 3.09 (0.25), residues: 451 sheet: None (None), residues: 0 loop : -0.69 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 40 TYR 0.006 0.001 TYR A 235 PHE 0.019 0.001 PHE B 28 TRP 0.005 0.001 TRP B 60 HIS 0.002 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 4445) covalent geometry : angle 0.42525 / 0.25 ( 6071) hydrogen bonds : bond 0.12775 / 8.55 ( 377) hydrogen bonds : angle 5.14820 / 3.66 ( 1122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 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 SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 145 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 LYS 300 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 7 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 LYS 55 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 91 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 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. Evaluate side-chains 157 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8159 (mmm) cc_final: 0.7949 (mmt) REVERT: A 33 LYS cc_start: 0.7936 (tttm) cc_final: 0.7603 (tptt) REVERT: A 60 TRP cc_start: 0.7744 (m100) cc_final: 0.7132 (m-10) REVERT: A 66 MET cc_start: 0.8758 (ttp) cc_final: 0.7786 (tmm) REVERT: A 113 LYS cc_start: 0.8904 (tttt) cc_final: 0.8615 (ttmm) REVERT: A 133 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8167 (pm20) REVERT: A 263 CYS cc_start: 0.8798 (t) cc_final: 0.8508 (t) REVERT: B 172 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6436 (mpt180) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1029 time to fit residues: 20.9882 Evaluate side-chains 129 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141290 restraints weight = 22461.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.146931 restraints weight = 8975.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.150541 restraints weight = 4883.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.152896 restraints weight = 3188.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154381 restraints weight = 2317.116| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4445 Z= 0.198 Angle : 0.533 6.565 6071 Z= 0.306 Chirality : 0.036 0.152 751 Planarity : 0.005 0.050 743 Dihedral : 3.698 21.689 632 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.06 % Allowed : 12.94 % Favored : 84.00 % 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: 3.12 (0.36), residues: 601 helix: 2.76 (0.25), residues: 462 sheet: None (None), residues: 0 loop : -0.45 (0.58), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 40 TYR 0.007 0.001 TYR B 53 PHE 0.016 0.001 PHE B 28 TRP 0.004 0.001 TRP B 57 HIS 0.010 0.002 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 ( 4445) covalent geometry : angle 0.53278 / 0.31 ( 6071) hydrogen bonds : bond 0.04862 / 3.17 ( 377) hydrogen bonds : angle 4.82845 / 3.50 ( 1122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 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 SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 145 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 LYS 300 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 7 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 LYS 55 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 91 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 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. Evaluate side-chains 149 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8268 (mmm) cc_final: 0.7993 (mmt) REVERT: A 33 LYS cc_start: 0.8099 (tttm) cc_final: 0.7732 (tptt) REVERT: A 58 LEU cc_start: 0.8301 (tp) cc_final: 0.7816 (tt) REVERT: A 60 TRP cc_start: 0.7894 (m100) cc_final: 0.7350 (t60) REVERT: A 66 MET cc_start: 0.8781 (ttp) cc_final: 0.7831 (tmm) REVERT: A 70 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 113 LYS cc_start: 0.8939 (tttt) cc_final: 0.8647 (ttmm) REVERT: A 133 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8230 (pm20) REVERT: A 263 CYS cc_start: 0.8811 (t) cc_final: 0.8544 (t) REVERT: A 297 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7964 (m-70) REVERT: B 66 MET cc_start: 0.7295 (ttm) cc_final: 0.6917 (tpt) REVERT: B 172 ARG cc_start: 0.7327 (mmm-85) cc_final: 0.6520 (mpt180) outliers start: 13 outliers final: 10 residues processed: 141 average time/residue: 0.1126 time to fit residues: 20.9276 Evaluate side-chains 139 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.169127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.146229 restraints weight = 22667.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.151901 restraints weight = 9387.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155644 restraints weight = 5364.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.157977 restraints weight = 3654.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.159641 restraints weight = 2792.272| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4445 Z= 0.145 Angle : 0.478 6.438 6071 Z= 0.272 Chirality : 0.035 0.146 751 Planarity : 0.004 0.039 743 Dihedral : 3.719 21.565 632 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.59 % Allowed : 14.35 % Favored : 83.06 % 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: 3.10 (0.36), residues: 601 helix: 2.77 (0.25), residues: 461 sheet: None (None), residues: 0 loop : -0.51 (0.57), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.006 0.001 TYR B 53 PHE 0.015 0.001 PHE B 28 TRP 0.004 0.001 TRP B 59 HIS 0.008 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 4445) covalent geometry : angle 0.47839 / 0.27 ( 6071) hydrogen bonds : bond 0.04431 / 2.91 ( 377) hydrogen bonds : angle 4.53730 / 3.26 ( 1122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 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 SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 145 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 LYS 300 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 7 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 LYS 55 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 91 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 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. Evaluate side-chains 144 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8203 (mmm) cc_final: 0.7941 (mmt) REVERT: A 33 LYS cc_start: 0.8106 (tttm) cc_final: 0.7738 (tptt) REVERT: A 58 LEU cc_start: 0.8154 (tp) cc_final: 0.7531 (tt) REVERT: A 60 TRP cc_start: 0.7908 (m100) cc_final: 0.7385 (t60) REVERT: A 66 MET cc_start: 0.8721 (ttp) cc_final: 0.7878 (tmm) REVERT: A 70 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 113 LYS cc_start: 0.8883 (tttt) cc_final: 0.8618 (ttmm) REVERT: A 133 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8200 (pm20) REVERT: A 263 CYS cc_start: 0.8780 (t) cc_final: 0.8550 (t) REVERT: B 66 MET cc_start: 0.7194 (ttm) cc_final: 0.6865 (tpt) REVERT: B 172 ARG cc_start: 0.7185 (mmm-85) cc_final: 0.6406 (mpt180) outliers start: 11 outliers final: 11 residues processed: 136 average time/residue: 0.1199 time to fit residues: 21.0836 Evaluate side-chains 139 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.167236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.144844 restraints weight = 22884.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.150534 restraints weight = 9560.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.154118 restraints weight = 5480.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.156514 restraints weight = 3757.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.158123 restraints weight = 2852.579| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4445 Z= 0.135 Angle : 0.473 6.331 6071 Z= 0.265 Chirality : 0.035 0.147 751 Planarity : 0.004 0.038 743 Dihedral : 3.660 21.324 632 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.35 % Allowed : 15.29 % Favored : 82.35 % 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: 3.16 (0.37), residues: 601 helix: 2.80 (0.25), residues: 461 sheet: None (None), residues: 0 loop : -0.45 (0.58), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 40 TYR 0.012 0.001 TYR B 53 PHE 0.015 0.001 PHE B 28 TRP 0.004 0.001 TRP A 59 HIS 0.011 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 4445) covalent geometry : angle 0.47289 / 0.27 ( 6071) hydrogen bonds : bond 0.04212 / 2.77 ( 377) hydrogen bonds : angle 4.41576 / 3.17 ( 1122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 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 SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 145 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 LYS 300 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 7 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 LYS 55 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 91 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 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. Evaluate side-chains 137 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8180 (mmm) cc_final: 0.7924 (mmt) REVERT: A 33 LYS cc_start: 0.8070 (tttm) cc_final: 0.7761 (tptt) REVERT: A 60 TRP cc_start: 0.7924 (m100) cc_final: 0.7390 (t60) REVERT: A 66 MET cc_start: 0.8783 (ttp) cc_final: 0.7899 (tmm) REVERT: A 70 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 113 LYS cc_start: 0.8846 (tttt) cc_final: 0.8598 (ttmm) REVERT: A 263 CYS cc_start: 0.8762 (t) cc_final: 0.8531 (t) REVERT: B 66 MET cc_start: 0.7179 (ttm) cc_final: 0.6837 (tpt) REVERT: B 172 ARG cc_start: 0.7184 (mmm-85) cc_final: 0.6382 (mpt180) outliers start: 10 outliers final: 8 residues processed: 131 average time/residue: 0.1185 time to fit residues: 20.4027 Evaluate side-chains 135 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 37 optimal weight: 0.7980 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.168004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.148086 restraints weight = 22282.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153496 restraints weight = 8876.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156948 restraints weight = 4811.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.159217 restraints weight = 3140.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160803 restraints weight = 2290.903| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4445 Z= 0.139 Angle : 0.472 6.290 6071 Z= 0.265 Chirality : 0.035 0.148 751 Planarity : 0.004 0.057 743 Dihedral : 3.678 21.202 632 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.35 % Allowed : 16.00 % Favored : 81.65 % 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: 3.13 (0.36), residues: 601 helix: 2.78 (0.25), residues: 461 sheet: None (None), residues: 0 loop : -0.43 (0.59), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 40 TYR 0.005 0.001 TYR B 53 PHE 0.015 0.001 PHE B 28 TRP 0.005 0.001 TRP A 59 HIS 0.008 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 4445) covalent geometry : angle 0.47238 / 0.27 ( 6071) hydrogen bonds : bond 0.04160 / 2.74 ( 377) hydrogen bonds : angle 4.38240 / 3.14 ( 1122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 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 SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 145 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 LYS 300 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 7 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 LYS 55 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 91 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 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. Evaluate side-chains 136 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8162 (mmm) cc_final: 0.7891 (mmt) REVERT: A 33 LYS cc_start: 0.8072 (tttm) cc_final: 0.7765 (tptt) REVERT: A 60 TRP cc_start: 0.7923 (m100) cc_final: 0.7387 (t60) REVERT: A 66 MET cc_start: 0.8759 (ttp) cc_final: 0.7934 (tmm) REVERT: A 70 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7812 (mm-30) REVERT: A 113 LYS cc_start: 0.8859 (tttt) cc_final: 0.8584 (ttmm) REVERT: A 232 GLN cc_start: 0.8316 (tt0) cc_final: 0.7919 (mt0) REVERT: A 263 CYS cc_start: 0.8731 (t) cc_final: 0.8502 (t) REVERT: B 66 MET cc_start: 0.7194 (ttm) cc_final: 0.6865 (tpt) REVERT: B 172 ARG cc_start: 0.7131 (mmm-85) cc_final: 0.6347 (mpt180) REVERT: B 259 SER cc_start: 0.9300 (m) cc_final: 0.8774 (t) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.1113 time to fit residues: 18.9041 Evaluate side-chains 133 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.165801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143683 restraints weight = 22855.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149250 restraints weight = 9688.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152881 restraints weight = 5567.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154873 restraints weight = 3789.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.156678 restraints weight = 2971.174| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4445 Z= 0.171 Angle : 0.495 6.267 6071 Z= 0.282 Chirality : 0.035 0.150 751 Planarity : 0.004 0.037 743 Dihedral : 3.742 21.769 632 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.88 % Allowed : 17.65 % Favored : 80.47 % 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: 3.00 (0.36), residues: 601 helix: 2.68 (0.25), residues: 461 sheet: None (None), residues: 0 loop : -0.49 (0.58), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 214 TYR 0.006 0.001 TYR A 252 PHE 0.016 0.001 PHE B 28 TRP 0.006 0.001 TRP A 59 HIS 0.006 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 ( 4445) covalent geometry : angle 0.49454 / 0.28 ( 6071) hydrogen bonds : bond 0.04252 / 2.78 ( 377) hydrogen bonds : angle 4.46681 / 3.21 ( 1122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 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 SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 145 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 LYS 300 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 7 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 LYS 55 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 91 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 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. Evaluate side-chains 135 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8198 (mmm) cc_final: 0.7924 (mmt) REVERT: A 33 LYS cc_start: 0.8081 (tttm) cc_final: 0.7763 (tptt) REVERT: A 66 MET cc_start: 0.8729 (ttp) cc_final: 0.7966 (tmm) REVERT: A 70 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 113 LYS cc_start: 0.8855 (tttt) cc_final: 0.8597 (ttmm) REVERT: A 232 GLN cc_start: 0.8351 (tt0) cc_final: 0.7921 (mt0) REVERT: A 263 CYS cc_start: 0.8741 (t) cc_final: 0.8510 (t) REVERT: B 66 MET cc_start: 0.7288 (ttm) cc_final: 0.6852 (tpt) REVERT: B 172 ARG cc_start: 0.7202 (mmm-85) cc_final: 0.6403 (mpt180) REVERT: B 259 SER cc_start: 0.9317 (m) cc_final: 0.8790 (t) outliers start: 8 outliers final: 8 residues processed: 130 average time/residue: 0.1129 time to fit residues: 19.2573 Evaluate side-chains 132 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.167035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145359 restraints weight = 23150.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.150907 restraints weight = 9729.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.154466 restraints weight = 5569.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.156854 restraints weight = 3794.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.158176 restraints weight = 2851.455| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4445 Z= 0.155 Angle : 0.490 6.245 6071 Z= 0.278 Chirality : 0.035 0.149 751 Planarity : 0.004 0.036 743 Dihedral : 3.740 22.016 632 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.35 % Allowed : 16.71 % Favored : 80.94 % 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: 3.02 (0.36), residues: 601 helix: 2.72 (0.25), residues: 461 sheet: None (None), residues: 0 loop : -0.57 (0.58), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 40 TYR 0.006 0.001 TYR A 252 PHE 0.016 0.001 PHE B 28 TRP 0.006 0.001 TRP A 59 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 4445) covalent geometry : angle 0.49000 / 0.28 ( 6071) hydrogen bonds : bond 0.04210 / 2.77 ( 377) hydrogen bonds : angle 4.43525 / 3.17 ( 1122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 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 SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 145 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 LYS 300 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 7 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 LYS 55 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 91 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 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. Evaluate side-chains 138 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8157 (mmm) cc_final: 0.7851 (mmt) REVERT: A 33 LYS cc_start: 0.8091 (tttm) cc_final: 0.7773 (tptt) REVERT: A 66 MET cc_start: 0.8729 (ttp) cc_final: 0.7956 (tmm) REVERT: A 70 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 113 LYS cc_start: 0.8786 (tttt) cc_final: 0.8557 (ttmm) REVERT: A 232 GLN cc_start: 0.8454 (tt0) cc_final: 0.8054 (mt0) REVERT: A 253 TYR cc_start: 0.9343 (t80) cc_final: 0.9087 (t80) REVERT: A 263 CYS cc_start: 0.8721 (t) cc_final: 0.8493 (t) REVERT: B 66 MET cc_start: 0.7250 (ttm) cc_final: 0.6813 (tpt) REVERT: B 172 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6381 (mpt180) REVERT: B 259 SER cc_start: 0.9328 (m) cc_final: 0.8797 (t) outliers start: 10 outliers final: 9 residues processed: 132 average time/residue: 0.0962 time to fit residues: 16.6915 Evaluate side-chains 133 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.167399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145637 restraints weight = 23072.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.151254 restraints weight = 9706.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.154871 restraints weight = 5551.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157197 restraints weight = 3770.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.158671 restraints weight = 2846.792| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4445 Z= 0.140 Angle : 0.489 6.164 6071 Z= 0.273 Chirality : 0.035 0.147 751 Planarity : 0.005 0.065 743 Dihedral : 3.717 21.804 632 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.35 % Allowed : 17.18 % Favored : 80.47 % 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: 3.07 (0.36), residues: 601 helix: 2.76 (0.25), residues: 461 sheet: None (None), residues: 0 loop : -0.59 (0.58), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 40 TYR 0.006 0.001 TYR A 235 PHE 0.016 0.001 PHE B 28 TRP 0.009 0.001 TRP A 59 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 4445) covalent geometry : angle 0.48870 / 0.27 ( 6071) hydrogen bonds : bond 0.04133 / 2.72 ( 377) hydrogen bonds : angle 4.35492 / 3.11 ( 1122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 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 SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 145 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 LYS 300 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 7 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 LYS 55 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 91 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 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. Evaluate side-chains 134 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8194 (mmm) cc_final: 0.7883 (mmt) REVERT: A 33 LYS cc_start: 0.8072 (tttm) cc_final: 0.7757 (tptt) REVERT: A 66 MET cc_start: 0.8721 (ttp) cc_final: 0.7957 (tmm) REVERT: A 70 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 113 LYS cc_start: 0.8773 (tttt) cc_final: 0.8545 (ttmm) REVERT: A 232 GLN cc_start: 0.8471 (tt0) cc_final: 0.8057 (mt0) REVERT: A 253 TYR cc_start: 0.9367 (t80) cc_final: 0.9126 (t80) REVERT: A 263 CYS cc_start: 0.8739 (t) cc_final: 0.8523 (t) REVERT: B 66 MET cc_start: 0.7264 (ttm) cc_final: 0.6804 (tpt) REVERT: B 172 ARG cc_start: 0.7194 (mmm-85) cc_final: 0.6411 (mpt180) REVERT: B 259 SER cc_start: 0.9309 (m) cc_final: 0.8774 (t) outliers start: 10 outliers final: 10 residues processed: 127 average time/residue: 0.1176 time to fit residues: 19.5679 Evaluate side-chains 133 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 37 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.167385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.145482 restraints weight = 22929.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.151092 restraints weight = 9582.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154735 restraints weight = 5478.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157104 restraints weight = 3720.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.158539 restraints weight = 2800.780| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4445 Z= 0.139 Angle : 0.487 6.122 6071 Z= 0.273 Chirality : 0.036 0.164 751 Planarity : 0.004 0.036 743 Dihedral : 3.669 21.817 632 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.35 % Allowed : 17.65 % Favored : 80.00 % 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: 3.10 (0.37), residues: 601 helix: 2.78 (0.25), residues: 462 sheet: None (None), residues: 0 loop : -0.57 (0.59), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.005 0.001 TYR A 252 PHE 0.016 0.001 PHE B 28 TRP 0.009 0.001 TRP A 59 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 4445) covalent geometry : angle 0.48715 / 0.27 ( 6071) hydrogen bonds : bond 0.04068 / 2.68 ( 377) hydrogen bonds : angle 4.34497 / 3.10 ( 1122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 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 SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 145 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 LYS 300 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 7 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 LYS 55 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 91 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 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. Evaluate side-chains 132 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8150 (mmm) cc_final: 0.7843 (mmt) REVERT: A 33 LYS cc_start: 0.8075 (tttm) cc_final: 0.7763 (tptt) REVERT: A 66 MET cc_start: 0.8704 (ttp) cc_final: 0.7943 (tmm) REVERT: A 70 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 232 GLN cc_start: 0.8420 (tt0) cc_final: 0.8012 (mt0) REVERT: A 253 TYR cc_start: 0.9356 (t80) cc_final: 0.9127 (t80) REVERT: A 263 CYS cc_start: 0.8706 (t) cc_final: 0.8487 (t) REVERT: B 66 MET cc_start: 0.7249 (ttm) cc_final: 0.6813 (tpt) REVERT: B 172 ARG cc_start: 0.7163 (mmm-85) cc_final: 0.6404 (mpt180) REVERT: B 259 SER cc_start: 0.9339 (m) cc_final: 0.8806 (t) outliers start: 10 outliers final: 10 residues processed: 126 average time/residue: 0.1247 time to fit residues: 20.5037 Evaluate side-chains 129 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.166786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147326 restraints weight = 22392.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.152657 restraints weight = 8730.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155972 restraints weight = 4718.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158255 restraints weight = 3097.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.159773 restraints weight = 2249.556| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4445 Z= 0.151 Angle : 0.499 6.175 6071 Z= 0.278 Chirality : 0.036 0.149 751 Planarity : 0.004 0.036 743 Dihedral : 3.707 22.014 632 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.12 % Allowed : 17.65 % Favored : 80.24 % 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: 3.04 (0.37), residues: 601 helix: 2.74 (0.25), residues: 463 sheet: None (None), residues: 0 loop : -0.63 (0.59), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 40 TYR 0.008 0.001 TYR A 235 PHE 0.016 0.001 PHE B 28 TRP 0.010 0.001 TRP A 59 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 4445) covalent geometry : angle 0.49872 / 0.28 ( 6071) hydrogen bonds : bond 0.04114 / 2.70 ( 377) hydrogen bonds : angle 4.36206 / 3.12 ( 1122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 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 SER 43 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 145 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 LYS 300 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 7 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 LYS 55 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue LEU 91 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 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. Evaluate side-chains 132 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8161 (mmm) cc_final: 0.7855 (mmt) REVERT: A 33 LYS cc_start: 0.8084 (tttm) cc_final: 0.7743 (tptt) REVERT: A 66 MET cc_start: 0.8701 (ttp) cc_final: 0.7956 (tmm) REVERT: A 70 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7671 (mm-30) REVERT: A 232 GLN cc_start: 0.8463 (tt0) cc_final: 0.8081 (mt0) REVERT: A 253 TYR cc_start: 0.9360 (t80) cc_final: 0.9133 (t80) REVERT: A 263 CYS cc_start: 0.8703 (t) cc_final: 0.8487 (t) REVERT: B 66 MET cc_start: 0.7295 (ttm) cc_final: 0.6854 (tpt) REVERT: B 172 ARG cc_start: 0.7113 (mmm-85) cc_final: 0.6374 (mpt180) REVERT: B 259 SER cc_start: 0.9339 (m) cc_final: 0.8815 (t) outliers start: 9 outliers final: 9 residues processed: 126 average time/residue: 0.1078 time to fit residues: 17.9442 Evaluate side-chains 130 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 0.0370 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.0470 chunk 37 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.169657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147856 restraints weight = 22613.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.153530 restraints weight = 9481.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.157231 restraints weight = 5382.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.159596 restraints weight = 3630.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.161145 restraints weight = 2726.972| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4445 Z= 0.113 Angle : 0.479 6.031 6071 Z= 0.262 Chirality : 0.037 0.191 751 Planarity : 0.004 0.034 743 Dihedral : 3.579 20.993 632 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.12 % Allowed : 18.12 % Favored : 79.76 % 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: 3.31 (0.37), residues: 601 helix: 2.92 (0.25), residues: 463 sheet: None (None), residues: 0 loop : -0.49 (0.60), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 40 TYR 0.007 0.001 TYR A 77 PHE 0.015 0.001 PHE B 28 TRP 0.013 0.001 TRP A 59 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 4445) covalent geometry : angle 0.47948 / 0.26 ( 6071) hydrogen bonds : bond 0.03830 / 2.54 ( 377) hydrogen bonds : angle 4.17255 / 2.96 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1540.20 seconds wall clock time: 26 minutes 50.44 seconds (1610.44 seconds total)