Starting phenix.real_space_refine on Fri Jun 6 16:44:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbj_39903/06_2025/8zbj_39903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbj_39903/06_2025/8zbj_39903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zbj_39903/06_2025/8zbj_39903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbj_39903/06_2025/8zbj_39903.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbj_39903/06_2025/8zbj_39903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbj_39903/06_2025/8zbj_39903.cif" } resolution = 2.94 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= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5168 2.51 5 N 1387 2.21 5 O 1472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8085 Number of models: 1 Model: "" Number of chains: 6 Chain: "S" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 78 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "C" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "E" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 419 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "F" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1689 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain breaks: 2 Chain: "R" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2034 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 249} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1281 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 166} Chain breaks: 5 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 5.13, per 1000 atoms: 0.63 Number of scatterers: 8085 At special positions: 0 Unit cell: (106.848, 106.848, 122.112, 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 58 16.00 O 1472 8.00 N 1387 7.00 C 5168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 197 " - pdb=" SG CYS F 267 " distance=2.04 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 36.6% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'C' and resid 6 through 26 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.647A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 24 removed outlier: 4.058A pdb=" N LYS E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'F' and resid 66 through 70 Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.790A pdb=" N THR F 129 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 67 removed outlier: 3.907A pdb=" N VAL R 45 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU R 48 " --> pdb=" O PRO R 44 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG R 67 " --> pdb=" O TYR R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 92 removed outlier: 3.694A pdb=" N ASN R 81 " --> pdb=" O ILE R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 103 removed outlier: 3.709A pdb=" N ALA R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 143 removed outlier: 3.841A pdb=" N LEU R 114 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR R 117 " --> pdb=" O ARG R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 170 removed outlier: 3.650A pdb=" N MET R 170 " --> pdb=" O LEU R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 178 Processing helix chain 'R' and resid 193 through 207 removed outlier: 3.795A pdb=" N TRP R 197 " --> pdb=" O PRO R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 229 removed outlier: 3.726A pdb=" N ILE R 224 " --> pdb=" O CYS R 220 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL R 225 " --> pdb=" O TYR R 221 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 274 removed outlier: 3.698A pdb=" N LYS R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG R 248 " --> pdb=" O ARG R 244 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) Proline residue: R 263 - end of helix removed outlier: 3.735A pdb=" N VAL R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 306 removed outlier: 3.889A pdb=" N ASN R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 316 removed outlier: 3.546A pdb=" N GLN R 313 " --> pdb=" O ASP R 309 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN R 316 " --> pdb=" O ARG R 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.541A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.892A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 removed outlier: 4.160A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.637A pdb=" N GLY C 330 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.930A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.762A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.813A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.636A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.443A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.433A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 285 " --> pdb=" O TRP C 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 41 through 46 removed outlier: 3.630A pdb=" N SER F 59 " --> pdb=" O SER F 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.198A pdb=" N GLY F 48 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET F 72 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR F 88 " --> pdb=" O MET F 72 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP F 74 " --> pdb=" O VAL F 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 178 through 179 Processing sheet with id=AB2, first strand: chain 'F' and resid 232 through 233 removed outlier: 6.720A pdb=" N TRP F 214 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR F 228 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU F 212 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.525A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1056 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: 2.48 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1640 1.33 - 1.45: 2021 1.45 - 1.57: 4508 1.57 - 1.69: 1 1.69 - 1.82: 83 Bond restraints: 8253 Sorted by residual: bond pdb=" N LYS S 9 " pdb=" CA LYS S 9 " ideal model delta sigma weight residual 1.457 1.405 0.052 1.29e-02 6.01e+03 1.64e+01 bond pdb=" C TRP S 8 " pdb=" O TRP S 8 " ideal model delta sigma weight residual 1.234 1.207 0.027 1.20e-02 6.94e+03 5.18e+00 bond pdb=" CB PRO C 194 " pdb=" CG PRO C 194 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.44e+00 bond pdb=" C LEU R 172 " pdb=" N PRO R 173 " ideal model delta sigma weight residual 1.335 1.364 -0.028 1.36e-02 5.41e+03 4.31e+00 bond pdb=" C TRP S 8 " pdb=" N LYS S 9 " ideal model delta sigma weight residual 1.332 1.308 0.025 1.40e-02 5.10e+03 3.08e+00 ... (remaining 8248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 11058 2.50 - 5.00: 100 5.00 - 7.50: 30 7.50 - 10.00: 7 10.00 - 12.50: 1 Bond angle restraints: 11196 Sorted by residual: angle pdb=" CA PRO C 194 " pdb=" N PRO C 194 " pdb=" CD PRO C 194 " ideal model delta sigma weight residual 112.00 103.65 8.35 1.40e+00 5.10e-01 3.56e+01 angle pdb=" C PHE S 7 " pdb=" N TRP S 8 " pdb=" CA TRP S 8 " ideal model delta sigma weight residual 120.82 127.36 -6.54 1.41e+00 5.03e-01 2.15e+01 angle pdb=" N PRO C 194 " pdb=" CD PRO C 194 " pdb=" CG PRO C 194 " ideal model delta sigma weight residual 103.20 96.60 6.60 1.50e+00 4.44e-01 1.93e+01 angle pdb=" N TRP S 8 " pdb=" CA TRP S 8 " pdb=" C TRP S 8 " ideal model delta sigma weight residual 110.10 116.28 -6.18 1.49e+00 4.50e-01 1.72e+01 angle pdb=" CA LEU R 172 " pdb=" CB LEU R 172 " pdb=" CG LEU R 172 " ideal model delta sigma weight residual 116.30 128.80 -12.50 3.50e+00 8.16e-02 1.28e+01 ... (remaining 11191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4139 17.05 - 34.09: 518 34.09 - 51.14: 150 51.14 - 68.19: 27 68.19 - 85.24: 12 Dihedral angle restraints: 4846 sinusoidal: 1827 harmonic: 3019 Sorted by residual: dihedral pdb=" CA LEU R 93 " pdb=" C LEU R 93 " pdb=" N PRO R 94 " pdb=" CA PRO R 94 " ideal model delta harmonic sigma weight residual -180.00 -158.99 -21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TYR F 139 " pdb=" C TYR F 139 " pdb=" N TYR F 140 " pdb=" CA TYR F 140 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA TYR F 273 " pdb=" C TYR F 273 " pdb=" N PRO F 274 " pdb=" CA PRO F 274 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 913 0.040 - 0.080: 268 0.080 - 0.119: 92 0.119 - 0.159: 14 0.159 - 0.199: 2 Chirality restraints: 1289 Sorted by residual: chirality pdb=" CA TRP S 8 " pdb=" N TRP S 8 " pdb=" C TRP S 8 " pdb=" CB TRP S 8 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA TYR F 273 " pdb=" N TYR F 273 " pdb=" C TYR F 273 " pdb=" CB TYR F 273 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA TYR C 59 " pdb=" N TYR C 59 " pdb=" C TYR C 59 " pdb=" CB TYR C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 1286 not shown) Planarity restraints: 1409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " -0.076 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO C 194 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 105 " -0.024 2.00e-02 2.50e+03 2.23e-02 1.24e+01 pdb=" CG TRP R 105 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP R 105 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP R 105 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 105 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 105 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 105 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 105 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP R 105 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 48 " -0.051 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO E 49 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 49 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 49 " -0.043 5.00e-02 4.00e+02 ... (remaining 1406 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1611 2.78 - 3.31: 7296 3.31 - 3.84: 12882 3.84 - 4.37: 14762 4.37 - 4.90: 26503 Nonbonded interactions: 63054 Sorted by model distance: nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP R 86 " pdb=" OG SER R 297 " model vdw 2.257 3.040 nonbonded pdb=" O ALA E 56 " pdb=" NH2 ARG E 62 " model vdw 2.262 3.120 nonbonded pdb=" O ALA C 257 " pdb=" NE2 GLN C 259 " model vdw 2.275 3.120 nonbonded pdb=" O SER R 146 " pdb=" NH1 ARG R 149 " model vdw 2.293 3.120 ... (remaining 63049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 23.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.360 Find NCS groups from input model: 0.060 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:22.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8255 Z= 0.164 Angle : 0.729 12.505 11200 Z= 0.373 Chirality : 0.043 0.199 1289 Planarity : 0.005 0.109 1409 Dihedral : 16.704 85.236 2888 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.46 % Rotamer: Outliers : 3.36 % Allowed : 31.37 % Favored : 65.28 % 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 (0.26), residues: 1017 helix: 1.90 (0.29), residues: 345 sheet: 0.16 (0.33), residues: 251 loop : -1.25 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP R 105 HIS 0.003 0.001 HIS C 183 PHE 0.028 0.002 PHE R 306 TYR 0.018 0.001 TYR R 294 ARG 0.007 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.16948 ( 379) hydrogen bonds : angle 5.62431 ( 1056) SS BOND : bond 0.00458 ( 2) SS BOND : angle 0.77882 ( 4) covalent geometry : bond 0.00349 ( 8253) covalent geometry : angle 0.72946 (11196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 212 ASP cc_start: 0.7104 (t70) cc_final: 0.6374 (t0) REVERT: C 215 GLU cc_start: 0.7822 (mp0) cc_final: 0.7168 (mp0) REVERT: C 325 MET cc_start: 0.8528 (tpp) cc_final: 0.8223 (tpp) outliers start: 29 outliers final: 24 residues processed: 135 average time/residue: 0.9651 time to fit residues: 140.1218 Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 340 ASN E 59 ASN F 115 ASN R 58 ASN ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.206607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141799 restraints weight = 9112.706| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.10 r_work: 0.3450 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8255 Z= 0.174 Angle : 0.666 10.513 11200 Z= 0.328 Chirality : 0.043 0.207 1289 Planarity : 0.005 0.065 1409 Dihedral : 7.068 59.484 1162 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 6.94 % Allowed : 25.58 % Favored : 67.48 % 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: 0.23 (0.26), residues: 1017 helix: 1.82 (0.28), residues: 351 sheet: 0.00 (0.32), residues: 255 loop : -1.23 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 105 HIS 0.005 0.001 HIS C 183 PHE 0.026 0.002 PHE C 199 TYR 0.018 0.002 TYR R 294 ARG 0.006 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04731 ( 379) hydrogen bonds : angle 4.60504 ( 1056) SS BOND : bond 0.00394 ( 2) SS BOND : angle 1.12667 ( 4) covalent geometry : bond 0.00412 ( 8253) covalent geometry : angle 0.66556 (11196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 116 time to evaluate : 0.955 Fit side-chains REVERT: C 212 ASP cc_start: 0.7637 (t70) cc_final: 0.7065 (t0) REVERT: C 215 GLU cc_start: 0.7816 (mp0) cc_final: 0.7324 (mp0) REVERT: C 255 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7967 (mp) REVERT: C 325 MET cc_start: 0.8624 (tpp) cc_final: 0.8302 (tpp) REVERT: F 115 ASN cc_start: 0.7809 (m-40) cc_final: 0.7591 (m-40) REVERT: F 198 ARG cc_start: 0.7266 (ttm110) cc_final: 0.6378 (mtm110) REVERT: F 261 ASP cc_start: 0.7562 (m-30) cc_final: 0.6492 (t0) REVERT: A 198 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7247 (tmm) REVERT: A 308 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7213 (mp0) outliers start: 60 outliers final: 32 residues processed: 155 average time/residue: 0.8623 time to fit residues: 145.2571 Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.208399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.140312 restraints weight = 9187.845| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.57 r_work: 0.3517 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8255 Z= 0.117 Angle : 0.595 9.844 11200 Z= 0.290 Chirality : 0.041 0.166 1289 Planarity : 0.004 0.050 1409 Dihedral : 5.882 57.577 1142 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Rotamer: Outliers : 6.13 % Allowed : 26.74 % Favored : 67.13 % 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: 0.33 (0.26), residues: 1017 helix: 1.96 (0.29), residues: 346 sheet: 0.00 (0.32), residues: 253 loop : -1.12 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 105 HIS 0.003 0.001 HIS C 183 PHE 0.016 0.001 PHE C 199 TYR 0.014 0.001 TYR F 228 ARG 0.004 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 379) hydrogen bonds : angle 4.39201 ( 1056) SS BOND : bond 0.00301 ( 2) SS BOND : angle 0.88616 ( 4) covalent geometry : bond 0.00268 ( 8253) covalent geometry : angle 0.59529 (11196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 0.923 Fit side-chains REVERT: C 212 ASP cc_start: 0.7577 (t70) cc_final: 0.7079 (t0) REVERT: C 215 GLU cc_start: 0.7858 (mp0) cc_final: 0.7412 (mp0) REVERT: C 217 MET cc_start: 0.7475 (ppp) cc_final: 0.7135 (pmt) REVERT: C 255 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7763 (mp) REVERT: C 325 MET cc_start: 0.8523 (tpp) cc_final: 0.8137 (tpp) REVERT: E 21 MET cc_start: 0.7093 (mpp) cc_final: 0.6625 (mpp) REVERT: F 198 ARG cc_start: 0.7261 (ttm110) cc_final: 0.6591 (mtp85) REVERT: F 230 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7482 (ptp) REVERT: F 261 ASP cc_start: 0.7578 (m-30) cc_final: 0.6564 (t0) REVERT: R 181 GLN cc_start: 0.4256 (OUTLIER) cc_final: 0.3815 (mt0) REVERT: A 198 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7160 (tmm) REVERT: A 308 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7177 (mp0) outliers start: 53 outliers final: 24 residues processed: 148 average time/residue: 0.8459 time to fit residues: 136.0098 Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 ASN F 151 GLN R 58 ASN ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.206910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142552 restraints weight = 9253.578| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.07 r_work: 0.3462 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8255 Z= 0.141 Angle : 0.622 11.615 11200 Z= 0.299 Chirality : 0.042 0.184 1289 Planarity : 0.004 0.052 1409 Dihedral : 5.608 57.866 1136 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Rotamer: Outliers : 6.37 % Allowed : 27.08 % Favored : 66.55 % 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: 0.32 (0.26), residues: 1017 helix: 2.00 (0.29), residues: 346 sheet: 0.01 (0.32), residues: 250 loop : -1.19 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 105 HIS 0.004 0.001 HIS F 73 PHE 0.021 0.001 PHE C 199 TYR 0.012 0.001 TYR F 228 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 379) hydrogen bonds : angle 4.35162 ( 1056) SS BOND : bond 0.00365 ( 2) SS BOND : angle 0.93105 ( 4) covalent geometry : bond 0.00330 ( 8253) covalent geometry : angle 0.62161 (11196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 104 time to evaluate : 0.959 Fit side-chains REVERT: C 212 ASP cc_start: 0.7591 (t70) cc_final: 0.7074 (t0) REVERT: C 215 GLU cc_start: 0.7885 (mp0) cc_final: 0.7399 (mp0) REVERT: C 217 MET cc_start: 0.7475 (ppp) cc_final: 0.7191 (pmt) REVERT: C 325 MET cc_start: 0.8595 (tpp) cc_final: 0.8199 (tpp) REVERT: F 115 ASN cc_start: 0.7884 (m-40) cc_final: 0.7651 (m-40) REVERT: F 230 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7503 (ptp) REVERT: F 261 ASP cc_start: 0.7560 (m-30) cc_final: 0.6501 (t0) REVERT: F 273 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.5418 (t80) REVERT: A 198 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7150 (tmm) REVERT: A 308 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7007 (mp0) outliers start: 55 outliers final: 30 residues processed: 144 average time/residue: 0.8195 time to fit residues: 128.3910 Evaluate side-chains 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.208036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140045 restraints weight = 9042.730| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.55 r_work: 0.3521 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8255 Z= 0.111 Angle : 0.598 11.380 11200 Z= 0.285 Chirality : 0.041 0.161 1289 Planarity : 0.004 0.049 1409 Dihedral : 5.169 58.607 1133 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.85 % Favored : 97.05 % Rotamer: Outliers : 7.06 % Allowed : 26.50 % Favored : 66.44 % 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: 0.38 (0.26), residues: 1017 helix: 2.01 (0.29), residues: 346 sheet: 0.10 (0.32), residues: 248 loop : -1.15 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 105 HIS 0.002 0.001 HIS C 183 PHE 0.019 0.001 PHE R 104 TYR 0.014 0.001 TYR R 294 ARG 0.010 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 379) hydrogen bonds : angle 4.25188 ( 1056) SS BOND : bond 0.00236 ( 2) SS BOND : angle 0.65902 ( 4) covalent geometry : bond 0.00250 ( 8253) covalent geometry : angle 0.59780 (11196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 112 time to evaluate : 0.864 Fit side-chains REVERT: C 134 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7760 (ptt-90) REVERT: C 212 ASP cc_start: 0.7458 (t70) cc_final: 0.7038 (t0) REVERT: C 215 GLU cc_start: 0.7912 (mp0) cc_final: 0.7455 (mp0) REVERT: C 217 MET cc_start: 0.7491 (ppp) cc_final: 0.7187 (pmt) REVERT: C 325 MET cc_start: 0.8506 (tpp) cc_final: 0.8122 (tpp) REVERT: E 21 MET cc_start: 0.6896 (mpp) cc_final: 0.6517 (mpp) REVERT: F 115 ASN cc_start: 0.7715 (m-40) cc_final: 0.7507 (m-40) REVERT: F 198 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6509 (mtp85) REVERT: F 230 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7496 (ptp) REVERT: F 261 ASP cc_start: 0.7570 (m-30) cc_final: 0.6583 (t0) REVERT: F 273 TYR cc_start: 0.5815 (OUTLIER) cc_final: 0.5249 (t80) REVERT: A 8 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: A 195 HIS cc_start: 0.6214 (OUTLIER) cc_final: 0.5943 (t-170) REVERT: A 198 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7225 (tmm) REVERT: A 308 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7138 (mp0) outliers start: 61 outliers final: 30 residues processed: 157 average time/residue: 0.8258 time to fit residues: 140.6726 Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.207569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139341 restraints weight = 9146.523| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.57 r_work: 0.3516 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8255 Z= 0.121 Angle : 0.617 13.529 11200 Z= 0.294 Chirality : 0.041 0.169 1289 Planarity : 0.004 0.052 1409 Dihedral : 5.012 58.705 1131 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 6.83 % Allowed : 27.31 % Favored : 65.86 % 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: 0.31 (0.26), residues: 1017 helix: 1.94 (0.28), residues: 346 sheet: 0.02 (0.32), residues: 252 loop : -1.16 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP R 105 HIS 0.003 0.001 HIS F 73 PHE 0.017 0.001 PHE C 199 TYR 0.017 0.001 TYR R 294 ARG 0.007 0.000 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 379) hydrogen bonds : angle 4.25098 ( 1056) SS BOND : bond 0.00321 ( 2) SS BOND : angle 0.74407 ( 4) covalent geometry : bond 0.00277 ( 8253) covalent geometry : angle 0.61743 (11196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 111 time to evaluate : 0.858 Fit side-chains REVERT: C 134 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7769 (ptt-90) REVERT: C 212 ASP cc_start: 0.7434 (t70) cc_final: 0.7072 (t0) REVERT: C 215 GLU cc_start: 0.7930 (mp0) cc_final: 0.7549 (mp0) REVERT: C 217 MET cc_start: 0.7475 (ppp) cc_final: 0.7163 (pmt) REVERT: C 325 MET cc_start: 0.8506 (tpp) cc_final: 0.8107 (tpp) REVERT: E 21 MET cc_start: 0.6984 (mpp) cc_final: 0.6581 (mpp) REVERT: F 198 ARG cc_start: 0.7144 (ttm110) cc_final: 0.6533 (mtp85) REVERT: F 230 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7480 (ptp) REVERT: F 261 ASP cc_start: 0.7686 (m-30) cc_final: 0.6529 (t0) REVERT: F 273 TYR cc_start: 0.5829 (OUTLIER) cc_final: 0.5252 (t80) REVERT: A 8 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: A 195 HIS cc_start: 0.6231 (OUTLIER) cc_final: 0.5991 (t-170) REVERT: A 198 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7277 (tmm) REVERT: A 308 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7124 (mp0) outliers start: 59 outliers final: 34 residues processed: 151 average time/residue: 0.8824 time to fit residues: 144.3485 Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 0.0060 chunk 22 optimal weight: 0.0870 chunk 54 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 ASN R 58 ASN R 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.209382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.139994 restraints weight = 9229.043| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.22 r_work: 0.3519 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8255 Z= 0.103 Angle : 0.609 11.218 11200 Z= 0.287 Chirality : 0.041 0.143 1289 Planarity : 0.004 0.051 1409 Dihedral : 4.814 59.497 1131 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.36 % Favored : 97.54 % Rotamer: Outliers : 5.56 % Allowed : 28.70 % Favored : 65.74 % 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: 0.43 (0.26), residues: 1017 helix: 2.01 (0.29), residues: 345 sheet: 0.19 (0.33), residues: 237 loop : -1.09 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP R 105 HIS 0.002 0.001 HIS F 73 PHE 0.018 0.001 PHE R 104 TYR 0.020 0.001 TYR R 294 ARG 0.006 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 379) hydrogen bonds : angle 4.19690 ( 1056) SS BOND : bond 0.00228 ( 2) SS BOND : angle 0.61431 ( 4) covalent geometry : bond 0.00226 ( 8253) covalent geometry : angle 0.60903 (11196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 0.825 Fit side-chains REVERT: C 212 ASP cc_start: 0.7401 (t70) cc_final: 0.7077 (t0) REVERT: C 215 GLU cc_start: 0.7925 (mp0) cc_final: 0.7548 (mp0) REVERT: C 217 MET cc_start: 0.7452 (ppp) cc_final: 0.7140 (pmt) REVERT: C 325 MET cc_start: 0.8508 (tpp) cc_final: 0.8117 (tpp) REVERT: E 21 MET cc_start: 0.6989 (mpp) cc_final: 0.6588 (mpp) REVERT: F 230 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7538 (ptp) REVERT: F 261 ASP cc_start: 0.7653 (m-30) cc_final: 0.6537 (t0) REVERT: F 273 TYR cc_start: 0.5503 (OUTLIER) cc_final: 0.5020 (t80) REVERT: R 158 LEU cc_start: 0.4805 (pp) cc_final: 0.4238 (mt) REVERT: A 195 HIS cc_start: 0.6184 (OUTLIER) cc_final: 0.5930 (t-170) REVERT: A 198 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7326 (tmm) REVERT: A 308 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7111 (mp0) outliers start: 48 outliers final: 27 residues processed: 145 average time/residue: 0.9063 time to fit residues: 142.5168 Evaluate side-chains 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 0.0170 chunk 34 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN F 115 ASN R 58 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.203069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.135509 restraints weight = 9193.120| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.54 r_work: 0.3477 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8255 Z= 0.164 Angle : 0.677 13.171 11200 Z= 0.324 Chirality : 0.043 0.195 1289 Planarity : 0.004 0.052 1409 Dihedral : 5.054 58.810 1131 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 6.60 % Allowed : 28.82 % Favored : 64.58 % 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: 0.30 (0.26), residues: 1017 helix: 1.93 (0.28), residues: 345 sheet: 0.15 (0.31), residues: 256 loop : -1.28 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP R 105 HIS 0.005 0.001 HIS F 73 PHE 0.019 0.002 PHE C 199 TYR 0.027 0.002 TYR R 294 ARG 0.011 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 379) hydrogen bonds : angle 4.33535 ( 1056) SS BOND : bond 0.00361 ( 2) SS BOND : angle 0.97562 ( 4) covalent geometry : bond 0.00394 ( 8253) covalent geometry : angle 0.67705 (11196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 103 time to evaluate : 0.928 Fit side-chains REVERT: C 212 ASP cc_start: 0.7427 (t70) cc_final: 0.7063 (t0) REVERT: C 215 GLU cc_start: 0.7956 (mp0) cc_final: 0.7482 (mp0) REVERT: C 217 MET cc_start: 0.7528 (ppp) cc_final: 0.7159 (pmt) REVERT: C 325 MET cc_start: 0.8562 (tpp) cc_final: 0.8201 (tpp) REVERT: E 21 MET cc_start: 0.7023 (mpp) cc_final: 0.6732 (mpp) REVERT: F 115 ASN cc_start: 0.7878 (m-40) cc_final: 0.7648 (m-40) REVERT: F 198 ARG cc_start: 0.7081 (ttm110) cc_final: 0.6358 (mtm110) REVERT: F 230 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7568 (ptp) REVERT: F 261 ASP cc_start: 0.7636 (m-30) cc_final: 0.6541 (t0) REVERT: F 273 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5471 (t80) REVERT: R 158 LEU cc_start: 0.4847 (pp) cc_final: 0.4283 (mt) REVERT: A 195 HIS cc_start: 0.6218 (OUTLIER) cc_final: 0.6008 (t-90) REVERT: A 198 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7198 (tmm) REVERT: A 308 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7094 (mp0) outliers start: 57 outliers final: 31 residues processed: 144 average time/residue: 1.0490 time to fit residues: 163.9529 Evaluate side-chains 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.204827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.140608 restraints weight = 9259.175| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.77 r_work: 0.3446 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8255 Z= 0.177 Angle : 0.705 12.157 11200 Z= 0.335 Chirality : 0.043 0.213 1289 Planarity : 0.004 0.049 1409 Dihedral : 5.137 57.449 1131 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 5.67 % Allowed : 30.32 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.26), residues: 1017 helix: 1.92 (0.28), residues: 345 sheet: -0.01 (0.32), residues: 252 loop : -1.33 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP R 105 HIS 0.004 0.001 HIS F 73 PHE 0.033 0.002 PHE R 315 TYR 0.023 0.002 TYR R 294 ARG 0.010 0.001 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 379) hydrogen bonds : angle 4.37575 ( 1056) SS BOND : bond 0.00427 ( 2) SS BOND : angle 1.03020 ( 4) covalent geometry : bond 0.00425 ( 8253) covalent geometry : angle 0.70511 (11196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 0.914 Fit side-chains REVERT: C 212 ASP cc_start: 0.7529 (t70) cc_final: 0.7169 (t0) REVERT: C 215 GLU cc_start: 0.7989 (mp0) cc_final: 0.7553 (mp0) REVERT: C 217 MET cc_start: 0.7664 (ppp) cc_final: 0.7319 (pmt) REVERT: C 325 MET cc_start: 0.8585 (tpp) cc_final: 0.8254 (tpp) REVERT: F 115 ASN cc_start: 0.7666 (m-40) cc_final: 0.7441 (m-40) REVERT: F 198 ARG cc_start: 0.7138 (ttm110) cc_final: 0.6424 (mtm110) REVERT: F 230 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7656 (ptp) REVERT: F 261 ASP cc_start: 0.7646 (m-30) cc_final: 0.6527 (t0) REVERT: F 273 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5604 (t80) REVERT: R 261 TRP cc_start: 0.7405 (OUTLIER) cc_final: 0.6727 (m-90) REVERT: A 195 HIS cc_start: 0.6139 (OUTLIER) cc_final: 0.5912 (t-90) REVERT: A 198 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7284 (tmm) REVERT: A 308 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7133 (mp0) outliers start: 49 outliers final: 33 residues processed: 136 average time/residue: 0.9280 time to fit residues: 136.3862 Evaluate side-chains 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 90 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN R 58 ASN R 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.206320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137836 restraints weight = 9082.123| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.55 r_work: 0.3469 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8255 Z= 0.132 Angle : 0.674 11.917 11200 Z= 0.317 Chirality : 0.042 0.191 1289 Planarity : 0.004 0.054 1409 Dihedral : 5.024 58.173 1131 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.75 % Favored : 97.15 % Rotamer: Outliers : 5.44 % Allowed : 30.67 % Favored : 63.89 % 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: 0.23 (0.26), residues: 1017 helix: 1.96 (0.28), residues: 345 sheet: 0.09 (0.32), residues: 250 loop : -1.36 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP R 105 HIS 0.003 0.001 HIS F 73 PHE 0.044 0.002 PHE R 315 TYR 0.022 0.001 TYR R 294 ARG 0.010 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 379) hydrogen bonds : angle 4.32096 ( 1056) SS BOND : bond 0.00336 ( 2) SS BOND : angle 0.87327 ( 4) covalent geometry : bond 0.00308 ( 8253) covalent geometry : angle 0.67430 (11196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 0.847 Fit side-chains REVERT: C 212 ASP cc_start: 0.7471 (t70) cc_final: 0.7081 (t0) REVERT: C 215 GLU cc_start: 0.7975 (mp0) cc_final: 0.7499 (mp0) REVERT: C 217 MET cc_start: 0.7676 (ppp) cc_final: 0.7329 (pmt) REVERT: C 325 MET cc_start: 0.8546 (tpp) cc_final: 0.8176 (tpp) REVERT: F 115 ASN cc_start: 0.7738 (m-40) cc_final: 0.7525 (m-40) REVERT: F 198 ARG cc_start: 0.7123 (ttm110) cc_final: 0.6509 (mtp85) REVERT: F 230 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7575 (ptp) REVERT: F 261 ASP cc_start: 0.7657 (m-30) cc_final: 0.6528 (t0) REVERT: F 273 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5443 (t80) REVERT: R 158 LEU cc_start: 0.4810 (pp) cc_final: 0.4260 (mt) REVERT: A 195 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.5934 (t-90) REVERT: A 198 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7283 (tmm) REVERT: A 308 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7140 (mp0) outliers start: 47 outliers final: 33 residues processed: 134 average time/residue: 0.9186 time to fit residues: 133.0281 Evaluate side-chains 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 286 TYR Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 96 optimal weight: 0.0030 chunk 37 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 0.0050 chunk 35 optimal weight: 5.9990 overall best weight: 1.1206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.206833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138770 restraints weight = 9286.716| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.08 r_work: 0.3431 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8255 Z= 0.131 Angle : 0.669 12.710 11200 Z= 0.312 Chirality : 0.042 0.181 1289 Planarity : 0.004 0.053 1409 Dihedral : 4.964 58.438 1131 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.85 % Favored : 97.05 % Rotamer: Outliers : 5.56 % Allowed : 30.21 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.26), residues: 1017 helix: 1.97 (0.28), residues: 346 sheet: 0.11 (0.32), residues: 250 loop : -1.34 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS F 73 PHE 0.028 0.001 PHE R 315 TYR 0.023 0.001 TYR R 294 ARG 0.010 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 379) hydrogen bonds : angle 4.27586 ( 1056) SS BOND : bond 0.00581 ( 2) SS BOND : angle 0.87119 ( 4) covalent geometry : bond 0.00305 ( 8253) covalent geometry : angle 0.66852 (11196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6667.01 seconds wall clock time: 115 minutes 57.26 seconds (6957.26 seconds total)