Starting phenix.real_space_refine on Wed Jun 11 02:17:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f34_28831/06_2025/8f34_28831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f34_28831/06_2025/8f34_28831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f34_28831/06_2025/8f34_28831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f34_28831/06_2025/8f34_28831.map" model { file = "/net/cci-nas-00/data/ceres_data/8f34_28831/06_2025/8f34_28831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f34_28831/06_2025/8f34_28831.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8180 2.51 5 N 2085 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12545 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D Time building chain proxies: 5.61, per 1000 atoms: 0.45 Number of scatterers: 12545 At special positions: 0 Unit cell: (88.038, 88.038, 122.859, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 2250 8.00 N 2085 7.00 C 8180 6.00 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: 3.20 Conformation dependent library (CDL) restraints added in 1.7 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 31.3% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.864A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 221 removed outlier: 3.819A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 225 Processing helix chain 'E' and resid 227 through 245 Processing helix chain 'E' and resid 260 through 286 Processing helix chain 'E' and resid 303 through 317 Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.864A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.819A pdb=" N LEU D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 227 through 245 Processing helix chain 'D' and resid 260 through 286 Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.863A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.819A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 227 through 245 Processing helix chain 'C' and resid 260 through 286 Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.863A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.819A pdb=" N LEU B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 227 through 245 Processing helix chain 'B' and resid 260 through 286 Processing helix chain 'B' and resid 303 through 317 Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.864A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.819A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 227 through 245 Processing helix chain 'A' and resid 260 through 286 Processing helix chain 'A' and resid 303 through 317 Processing sheet with id=AA1, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.289A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER E 84 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU E 107 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP E 86 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG E 105 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N GLY E 88 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N ASN E 103 " --> pdb=" O GLY E 88 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N LYS E 90 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N ILE E 101 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N LEU E 92 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N ARG E 99 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.628A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE E 188 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER E 171 " --> pdb=" O PHE E 188 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG E 190 " --> pdb=" O HIS E 169 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS E 169 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR E 192 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER E 167 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG E 194 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS E 165 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP E 196 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.289A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER D 84 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU D 107 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP D 86 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG D 105 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLY D 88 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N ASN D 103 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N LYS D 90 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N ILE D 101 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N LEU D 92 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N ARG D 99 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.628A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE D 188 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER D 171 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG D 190 " --> pdb=" O HIS D 169 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS D 169 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR D 192 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER D 167 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG D 194 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS D 165 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP D 196 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.289A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER C 84 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU C 107 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP C 86 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG C 105 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N GLY C 88 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N ASN C 103 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N LYS C 90 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 11.162A pdb=" N ILE C 101 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N LEU C 92 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N ARG C 99 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.629A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE C 188 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER C 171 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG C 190 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS C 169 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 192 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER C 167 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG C 194 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS C 165 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP C 196 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.289A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER B 84 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU B 107 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP B 86 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG B 105 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N GLY B 88 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N ASN B 103 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N LYS B 90 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 11.162A pdb=" N ILE B 101 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N LEU B 92 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N ARG B 99 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.628A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B 188 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER B 171 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 190 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS B 169 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 192 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 167 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG B 194 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS B 165 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP B 196 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.289A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER A 84 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU A 107 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP A 86 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG A 105 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLY A 88 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N ASN A 103 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N LYS A 90 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N ILE A 101 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N LEU A 92 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N ARG A 99 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.629A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 188 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER A 171 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG A 190 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS A 169 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR A 192 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER A 167 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG A 194 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS A 165 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP A 196 " --> pdb=" O ARG A 163 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3892 1.34 - 1.46: 2331 1.46 - 1.57: 6607 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12880 Sorted by residual: bond pdb=" CA TRP C 160 " pdb=" C TRP C 160 " ideal model delta sigma weight residual 1.526 1.507 0.020 1.03e-02 9.43e+03 3.64e+00 bond pdb=" CA TRP E 160 " pdb=" C TRP E 160 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.03e-02 9.43e+03 3.46e+00 bond pdb=" CA TRP A 160 " pdb=" C TRP A 160 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.03e-02 9.43e+03 3.43e+00 bond pdb=" CA TRP B 160 " pdb=" C TRP B 160 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.03e-02 9.43e+03 3.40e+00 bond pdb=" CA TRP D 160 " pdb=" C TRP D 160 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.03e-02 9.43e+03 3.39e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 16973 1.86 - 3.72: 477 3.72 - 5.58: 50 5.58 - 7.45: 35 7.45 - 9.31: 10 Bond angle restraints: 17545 Sorted by residual: angle pdb=" C ASN B 60 " pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C ASN E 60 " pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C ASN C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ASN A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ASN D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.33e+01 ... (remaining 17540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6751 17.83 - 35.65: 644 35.65 - 53.48: 120 53.48 - 71.31: 10 71.31 - 89.13: 5 Dihedral angle restraints: 7530 sinusoidal: 3025 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU B 118 " pdb=" C LEU B 118 " pdb=" N PHE B 119 " pdb=" CA PHE B 119 " ideal model delta harmonic sigma weight residual 180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU D 118 " pdb=" C LEU D 118 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N PHE A 119 " pdb=" CA PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1293 0.043 - 0.087: 396 0.087 - 0.130: 186 0.130 - 0.174: 59 0.174 - 0.217: 16 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CB ILE A 39 " pdb=" CA ILE A 39 " pdb=" CG1 ILE A 39 " pdb=" CG2 ILE A 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE E 39 " pdb=" CA ILE E 39 " pdb=" CG1 ILE E 39 " pdb=" CG2 ILE E 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 176 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" CG ASP D 176 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP D 176 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP D 176 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 176 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASP A 176 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP A 176 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 176 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 176 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASP B 176 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP B 176 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 176 " -0.014 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4129 2.85 - 3.36: 10943 3.36 - 3.87: 21234 3.87 - 4.39: 24673 4.39 - 4.90: 42404 Nonbonded interactions: 103383 Sorted by model distance: nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.333 3.040 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.334 3.040 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.334 3.040 nonbonded pdb=" O SER D 221 " pdb=" OG SER D 221 " model vdw 2.335 3.040 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.335 3.040 ... (remaining 103378 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.780 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12880 Z= 0.210 Angle : 0.770 9.307 17545 Z= 0.417 Chirality : 0.056 0.217 1950 Planarity : 0.005 0.046 2235 Dihedral : 14.077 89.134 4620 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1525 helix: 0.24 (0.23), residues: 500 sheet: 1.44 (0.25), residues: 460 loop : -3.01 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 206 HIS 0.002 0.001 HIS C 177 PHE 0.028 0.002 PHE C 116 TYR 0.022 0.002 TYR D 248 ARG 0.002 0.000 ARG D 299 Details of bonding type rmsd hydrogen bonds : bond 0.10650 ( 530) hydrogen bonds : angle 5.50754 ( 1545) covalent geometry : bond 0.00452 (12880) covalent geometry : angle 0.77038 (17545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.438 Fit side-chains REVERT: B 176 ASP cc_start: 0.7075 (t0) cc_final: 0.6855 (t0) REVERT: A 158 ASP cc_start: 0.6033 (p0) cc_final: 0.5282 (m-30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2779 time to fit residues: 64.3054 Evaluate side-chains 145 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.151163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117867 restraints weight = 13760.528| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.59 r_work: 0.3094 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12880 Z= 0.178 Angle : 0.619 8.718 17545 Z= 0.315 Chirality : 0.047 0.136 1950 Planarity : 0.004 0.035 2235 Dihedral : 4.997 49.776 1690 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.15 % Allowed : 6.76 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1525 helix: 0.91 (0.24), residues: 505 sheet: 1.68 (0.27), residues: 430 loop : -2.93 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 206 HIS 0.003 0.001 HIS A 284 PHE 0.020 0.002 PHE C 116 TYR 0.019 0.002 TYR C 248 ARG 0.002 0.000 ARG E 117 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 530) hydrogen bonds : angle 4.94522 ( 1545) covalent geometry : bond 0.00416 (12880) covalent geometry : angle 0.61931 (17545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 1.345 Fit side-chains REVERT: D 13 ASP cc_start: 0.8454 (m-30) cc_final: 0.8250 (m-30) REVERT: D 176 ASP cc_start: 0.7714 (t0) cc_final: 0.7354 (t0) REVERT: C 115 ASP cc_start: 0.7272 (t70) cc_final: 0.6725 (t70) REVERT: A 238 LEU cc_start: 0.7937 (mt) cc_final: 0.7719 (mt) outliers start: 2 outliers final: 1 residues processed: 154 average time/residue: 0.2088 time to fit residues: 49.2966 Evaluate side-chains 128 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 145 optimal weight: 10.0000 chunk 84 optimal weight: 0.0270 chunk 63 optimal weight: 0.3980 chunk 10 optimal weight: 7.9990 chunk 27 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.151590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119815 restraints weight = 13940.346| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.49 r_work: 0.3111 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12880 Z= 0.143 Angle : 0.553 8.204 17545 Z= 0.283 Chirality : 0.046 0.140 1950 Planarity : 0.003 0.033 2235 Dihedral : 4.730 42.403 1690 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.58 % Allowed : 12.58 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1525 helix: 1.07 (0.24), residues: 515 sheet: 1.66 (0.27), residues: 430 loop : -2.76 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 206 HIS 0.003 0.001 HIS D 284 PHE 0.015 0.001 PHE C 116 TYR 0.016 0.002 TYR A 248 ARG 0.002 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 530) hydrogen bonds : angle 4.69104 ( 1545) covalent geometry : bond 0.00329 (12880) covalent geometry : angle 0.55336 (17545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 1.466 Fit side-chains REVERT: E 238 LEU cc_start: 0.8021 (mt) cc_final: 0.7820 (mt) REVERT: C 174 ARG cc_start: 0.7736 (mtt-85) cc_final: 0.7532 (mmt180) REVERT: C 233 GLN cc_start: 0.6982 (tp40) cc_final: 0.6525 (mt0) REVERT: B 265 MET cc_start: 0.8356 (ttm) cc_final: 0.8115 (ttt) REVERT: A 115 ASP cc_start: 0.7317 (t0) cc_final: 0.6894 (t70) outliers start: 8 outliers final: 4 residues processed: 154 average time/residue: 0.2254 time to fit residues: 52.6459 Evaluate side-chains 142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain A residue 54 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 84 optimal weight: 0.0370 chunk 79 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 overall best weight: 3.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN B 151 ASN A 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.148447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115758 restraints weight = 13859.116| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.56 r_work: 0.3064 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12880 Z= 0.202 Angle : 0.624 9.422 17545 Z= 0.319 Chirality : 0.048 0.157 1950 Planarity : 0.003 0.034 2235 Dihedral : 4.985 41.481 1690 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.67 % Allowed : 14.47 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1525 helix: 1.10 (0.24), residues: 510 sheet: 1.47 (0.26), residues: 430 loop : -2.78 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 206 HIS 0.003 0.001 HIS D 284 PHE 0.016 0.002 PHE B 116 TYR 0.020 0.002 TYR E 248 ARG 0.002 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 530) hydrogen bonds : angle 4.90875 ( 1545) covalent geometry : bond 0.00475 (12880) covalent geometry : angle 0.62433 (17545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.348 Fit side-chains REVERT: E 31 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: E 161 TRP cc_start: 0.7754 (m-10) cc_final: 0.7499 (m-10) REVERT: E 163 ARG cc_start: 0.7083 (mmt180) cc_final: 0.6838 (mmt180) REVERT: E 238 LEU cc_start: 0.7976 (mt) cc_final: 0.7773 (mt) REVERT: D 151 ASN cc_start: 0.7794 (m110) cc_final: 0.7477 (m-40) REVERT: B 163 ARG cc_start: 0.7099 (mmt180) cc_final: 0.6883 (mmt180) REVERT: B 265 MET cc_start: 0.8363 (ttm) cc_final: 0.8112 (ttt) REVERT: A 31 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7324 (mt0) outliers start: 23 outliers final: 14 residues processed: 158 average time/residue: 0.2393 time to fit residues: 55.6140 Evaluate side-chains 160 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 64 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 111 optimal weight: 0.0970 chunk 71 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN E 284 HIS C 151 ASN C 284 HIS B 284 HIS A 284 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.148443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.115640 restraints weight = 13827.422| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.56 r_work: 0.3056 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12880 Z= 0.220 Angle : 0.642 9.741 17545 Z= 0.329 Chirality : 0.049 0.166 1950 Planarity : 0.004 0.035 2235 Dihedral : 5.123 42.278 1690 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.18 % Allowed : 17.67 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.23), residues: 1525 helix: 1.06 (0.24), residues: 505 sheet: 1.24 (0.26), residues: 430 loop : -2.87 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 206 HIS 0.003 0.001 HIS D 284 PHE 0.017 0.002 PHE C 116 TYR 0.021 0.002 TYR C 248 ARG 0.002 0.000 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 530) hydrogen bonds : angle 4.98537 ( 1545) covalent geometry : bond 0.00519 (12880) covalent geometry : angle 0.64239 (17545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.460 Fit side-chains REVERT: E 31 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: E 161 TRP cc_start: 0.7758 (m-10) cc_final: 0.7496 (m-10) REVERT: E 163 ARG cc_start: 0.6985 (mmt180) cc_final: 0.6710 (mmt180) REVERT: D 31 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.6886 (mt0) REVERT: D 151 ASN cc_start: 0.7785 (m110) cc_final: 0.7445 (m-40) REVERT: D 230 GLU cc_start: 0.5490 (mt-10) cc_final: 0.4665 (mm-30) REVERT: C 31 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7261 (mt0) REVERT: C 233 GLN cc_start: 0.6934 (tp40) cc_final: 0.6484 (mt0) REVERT: B 163 ARG cc_start: 0.7016 (mmt180) cc_final: 0.6769 (mmt180) REVERT: B 233 GLN cc_start: 0.6978 (tp40) cc_final: 0.6476 (mt0) REVERT: B 265 MET cc_start: 0.8373 (ttm) cc_final: 0.8126 (ttt) REVERT: A 31 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7284 (mt0) REVERT: A 163 ARG cc_start: 0.7085 (mmt180) cc_final: 0.6828 (mmt180) outliers start: 30 outliers final: 23 residues processed: 176 average time/residue: 0.2927 time to fit residues: 73.1334 Evaluate side-chains 174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 88 optimal weight: 0.0370 chunk 132 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.151780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.120152 restraints weight = 14021.296| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.49 r_work: 0.3112 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12880 Z= 0.120 Angle : 0.526 7.594 17545 Z= 0.268 Chirality : 0.045 0.129 1950 Planarity : 0.003 0.035 2235 Dihedral : 4.568 31.881 1690 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.82 % Allowed : 18.76 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1525 helix: 1.31 (0.24), residues: 515 sheet: 1.34 (0.26), residues: 435 loop : -2.69 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 206 HIS 0.003 0.001 HIS D 284 PHE 0.013 0.001 PHE A 116 TYR 0.012 0.001 TYR A 248 ARG 0.001 0.000 ARG E 117 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 530) hydrogen bonds : angle 4.63728 ( 1545) covalent geometry : bond 0.00272 (12880) covalent geometry : angle 0.52618 (17545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.426 Fit side-chains REVERT: E 144 ASP cc_start: 0.8036 (p0) cc_final: 0.7823 (p0) REVERT: E 161 TRP cc_start: 0.7762 (m-10) cc_final: 0.7546 (m-10) REVERT: E 163 ARG cc_start: 0.7046 (mmt180) cc_final: 0.6836 (mmt180) REVERT: D 117 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.5670 (mtt180) REVERT: D 151 ASN cc_start: 0.7807 (m110) cc_final: 0.7441 (m-40) REVERT: C 49 LYS cc_start: 0.7013 (tppt) cc_final: 0.5896 (tptt) REVERT: C 163 ARG cc_start: 0.7069 (mmt180) cc_final: 0.6810 (mmt180) REVERT: C 233 GLN cc_start: 0.6932 (tp40) cc_final: 0.6443 (mt0) REVERT: B 163 ARG cc_start: 0.7061 (mmt180) cc_final: 0.6853 (mmt180) REVERT: B 245 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.6396 (t80) REVERT: A 113 ASP cc_start: 0.7513 (m-30) cc_final: 0.7037 (p0) REVERT: A 163 ARG cc_start: 0.7142 (mmt180) cc_final: 0.6914 (mmt180) REVERT: A 233 GLN cc_start: 0.6931 (tp40) cc_final: 0.6482 (mt0) outliers start: 25 outliers final: 18 residues processed: 178 average time/residue: 0.2526 time to fit residues: 64.7966 Evaluate side-chains 169 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 14 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.148802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.116173 restraints weight = 13964.773| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.56 r_work: 0.3065 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12880 Z= 0.201 Angle : 0.614 9.177 17545 Z= 0.314 Chirality : 0.048 0.160 1950 Planarity : 0.003 0.036 2235 Dihedral : 4.930 35.528 1690 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.40 % Allowed : 18.98 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1525 helix: 1.20 (0.24), residues: 510 sheet: 1.22 (0.26), residues: 435 loop : -2.71 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 206 HIS 0.002 0.001 HIS D 284 PHE 0.015 0.002 PHE B 116 TYR 0.018 0.002 TYR E 248 ARG 0.002 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 530) hydrogen bonds : angle 4.84722 ( 1545) covalent geometry : bond 0.00472 (12880) covalent geometry : angle 0.61376 (17545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.601 Fit side-chains REVERT: E 161 TRP cc_start: 0.7758 (m-10) cc_final: 0.7511 (m-10) REVERT: E 163 ARG cc_start: 0.6990 (mmt180) cc_final: 0.6787 (mmt180) REVERT: D 117 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.5901 (mtt180) REVERT: D 151 ASN cc_start: 0.7821 (m110) cc_final: 0.7483 (m-40) REVERT: D 230 GLU cc_start: 0.5538 (mt-10) cc_final: 0.4722 (mm-30) REVERT: C 31 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7301 (mt0) REVERT: C 49 LYS cc_start: 0.6913 (tppt) cc_final: 0.5803 (tptt) REVERT: C 117 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.5790 (mtt180) REVERT: C 233 GLN cc_start: 0.6846 (tp40) cc_final: 0.6460 (mt0) REVERT: B 117 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.5792 (mtt180) REVERT: B 163 ARG cc_start: 0.6972 (mmt180) cc_final: 0.6745 (mmt180) REVERT: B 233 GLN cc_start: 0.7200 (tp40) cc_final: 0.6514 (mt0) REVERT: A 117 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.5844 (mtt180) REVERT: A 163 ARG cc_start: 0.7092 (mmt180) cc_final: 0.6863 (mmt180) REVERT: A 233 GLN cc_start: 0.6944 (tp40) cc_final: 0.6454 (mt0) outliers start: 33 outliers final: 17 residues processed: 181 average time/residue: 0.3344 time to fit residues: 84.6262 Evaluate side-chains 174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 7 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.149377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.116696 restraints weight = 14015.578| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.57 r_work: 0.3071 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12880 Z= 0.178 Angle : 0.597 8.821 17545 Z= 0.303 Chirality : 0.047 0.152 1950 Planarity : 0.003 0.036 2235 Dihedral : 4.866 33.463 1690 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.76 % Allowed : 18.84 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.23), residues: 1525 helix: 1.16 (0.24), residues: 515 sheet: 1.17 (0.26), residues: 435 loop : -2.70 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 206 HIS 0.002 0.001 HIS D 284 PHE 0.014 0.001 PHE B 116 TYR 0.017 0.002 TYR A 248 ARG 0.002 0.000 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 530) hydrogen bonds : angle 4.79721 ( 1545) covalent geometry : bond 0.00419 (12880) covalent geometry : angle 0.59707 (17545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 1.445 Fit side-chains REVERT: E 31 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: E 161 TRP cc_start: 0.7755 (m-10) cc_final: 0.7520 (m-10) REVERT: E 163 ARG cc_start: 0.6945 (mmt180) cc_final: 0.6695 (mmt180) REVERT: E 245 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.5545 (t80) REVERT: D 31 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.6775 (mt0) REVERT: D 117 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.5593 (mtt180) REVERT: D 151 ASN cc_start: 0.7804 (m110) cc_final: 0.7457 (m-40) REVERT: D 245 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.5798 (t80) REVERT: C 117 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.5492 (mtt180) REVERT: C 174 ARG cc_start: 0.7772 (mtt-85) cc_final: 0.7494 (mtp180) REVERT: C 233 GLN cc_start: 0.6839 (tp40) cc_final: 0.6473 (mt0) REVERT: C 245 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.6384 (t80) REVERT: B 117 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.5741 (mtt180) REVERT: B 163 ARG cc_start: 0.6928 (mmt180) cc_final: 0.6703 (mmt180) REVERT: B 233 GLN cc_start: 0.7132 (tp40) cc_final: 0.6498 (mt0) REVERT: A 117 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6335 (mpt180) REVERT: A 163 ARG cc_start: 0.7083 (mmt180) cc_final: 0.6860 (mmt180) REVERT: A 233 GLN cc_start: 0.6916 (tp40) cc_final: 0.6454 (mt0) REVERT: A 245 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.5516 (t80) outliers start: 38 outliers final: 20 residues processed: 184 average time/residue: 0.2928 time to fit residues: 75.8818 Evaluate side-chains 180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 1 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 24 optimal weight: 0.0070 chunk 64 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.150366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.117781 restraints weight = 13943.097| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.57 r_work: 0.3088 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12880 Z= 0.147 Angle : 0.566 8.220 17545 Z= 0.287 Chirality : 0.046 0.140 1950 Planarity : 0.003 0.036 2235 Dihedral : 4.696 31.344 1690 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.69 % Allowed : 18.98 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1525 helix: 1.28 (0.24), residues: 515 sheet: 1.25 (0.26), residues: 435 loop : -2.64 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 206 HIS 0.002 0.001 HIS D 284 PHE 0.014 0.001 PHE D 116 TYR 0.014 0.001 TYR A 248 ARG 0.001 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 530) hydrogen bonds : angle 4.69986 ( 1545) covalent geometry : bond 0.00341 (12880) covalent geometry : angle 0.56575 (17545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.446 Fit side-chains REVERT: E 161 TRP cc_start: 0.7723 (m-10) cc_final: 0.7477 (m-10) REVERT: E 245 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.5564 (t80) REVERT: D 31 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.6732 (mt0) REVERT: D 117 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.5561 (mtt180) REVERT: D 151 ASN cc_start: 0.7794 (m110) cc_final: 0.7432 (m-40) REVERT: D 245 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.5793 (t80) REVERT: C 31 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7298 (mt0) REVERT: C 117 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.5434 (mtt180) REVERT: C 174 ARG cc_start: 0.7787 (mtt-85) cc_final: 0.7526 (mtp180) REVERT: C 233 GLN cc_start: 0.6826 (tp40) cc_final: 0.6477 (mt0) REVERT: C 245 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6397 (t80) REVERT: B 117 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.5704 (mtt180) REVERT: B 163 ARG cc_start: 0.6933 (mmt180) cc_final: 0.6701 (mmt180) REVERT: B 233 GLN cc_start: 0.7127 (tp40) cc_final: 0.6513 (mt0) REVERT: B 245 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6284 (t80) REVERT: A 31 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: A 113 ASP cc_start: 0.7488 (m-30) cc_final: 0.7004 (p0) REVERT: A 117 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6339 (mpt180) REVERT: A 163 ARG cc_start: 0.7095 (mmt180) cc_final: 0.6871 (mmt180) REVERT: A 233 GLN cc_start: 0.6916 (tp40) cc_final: 0.6456 (mt0) REVERT: A 245 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.5541 (t80) outliers start: 37 outliers final: 20 residues processed: 181 average time/residue: 0.2735 time to fit residues: 69.6477 Evaluate side-chains 178 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.149735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.117205 restraints weight = 13903.833| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.56 r_work: 0.3081 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12880 Z= 0.162 Angle : 0.585 8.868 17545 Z= 0.298 Chirality : 0.047 0.146 1950 Planarity : 0.003 0.036 2235 Dihedral : 4.752 31.808 1690 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.91 % Allowed : 18.84 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1525 helix: 1.26 (0.24), residues: 515 sheet: 1.21 (0.26), residues: 435 loop : -2.62 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 206 HIS 0.002 0.001 HIS A 284 PHE 0.013 0.001 PHE C 116 TYR 0.016 0.002 TYR A 248 ARG 0.002 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 530) hydrogen bonds : angle 4.74653 ( 1545) covalent geometry : bond 0.00378 (12880) covalent geometry : angle 0.58531 (17545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.506 Fit side-chains REVERT: E 31 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: E 59 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8184 (mm-30) REVERT: E 161 TRP cc_start: 0.7717 (m-10) cc_final: 0.7496 (m-10) REVERT: E 245 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.5555 (t80) REVERT: D 31 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.6772 (mt0) REVERT: D 117 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.5610 (mtt180) REVERT: D 151 ASN cc_start: 0.7802 (m110) cc_final: 0.7450 (m-40) REVERT: D 245 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.5795 (t80) REVERT: C 31 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: C 117 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.5515 (mtt180) REVERT: C 174 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.7520 (mtp180) REVERT: C 233 GLN cc_start: 0.6838 (tp40) cc_final: 0.6455 (mt0) REVERT: C 245 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6403 (t80) REVERT: B 117 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.5774 (mtt180) REVERT: B 163 ARG cc_start: 0.6933 (mmt180) cc_final: 0.6700 (mmt180) REVERT: B 233 GLN cc_start: 0.7125 (tp40) cc_final: 0.6511 (mt0) REVERT: B 245 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.6283 (t80) REVERT: A 31 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: A 113 ASP cc_start: 0.7514 (m-30) cc_final: 0.7003 (p0) REVERT: A 117 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6352 (mpt180) REVERT: A 163 ARG cc_start: 0.7087 (mmt180) cc_final: 0.6864 (mmt180) REVERT: A 233 GLN cc_start: 0.6912 (tp40) cc_final: 0.6437 (mt0) REVERT: A 245 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.5552 (t80) outliers start: 40 outliers final: 23 residues processed: 178 average time/residue: 0.2775 time to fit residues: 69.3687 Evaluate side-chains 181 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.148540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115890 restraints weight = 14048.588| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.56 r_work: 0.3064 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12880 Z= 0.200 Angle : 0.627 9.559 17545 Z= 0.319 Chirality : 0.048 0.159 1950 Planarity : 0.003 0.036 2235 Dihedral : 4.959 33.845 1690 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.76 % Allowed : 19.20 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1525 helix: 1.19 (0.24), residues: 510 sheet: 1.11 (0.26), residues: 435 loop : -2.63 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 206 HIS 0.003 0.001 HIS A 284 PHE 0.015 0.002 PHE C 116 TYR 0.018 0.002 TYR A 248 ARG 0.002 0.000 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 530) hydrogen bonds : angle 4.86997 ( 1545) covalent geometry : bond 0.00472 (12880) covalent geometry : angle 0.62698 (17545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6574.15 seconds wall clock time: 115 minutes 15.82 seconds (6915.82 seconds total)