Starting phenix.real_space_refine on Sun May 11 11:37:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbj_39903/05_2025/8zbj_39903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbj_39903/05_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_39903/05_2025/8zbj_39903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbj_39903/05_2025/8zbj_39903.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbj_39903/05_2025/8zbj_39903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbj_39903/05_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-5687/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: 5.03, per 1000 atoms: 0.62 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: 1.84 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: 0.86 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: 2.06 Time building geometry restraints manager: 2.17 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: 0.750 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.480 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: 0.010 Load rotamer database and sin/cos tables:10.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- 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 : 0.799 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: 0.9122 time to fit residues: 132.6938 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 : 0.897 ------------------------------------------------------------------------------- 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 = 0.206606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141806 restraints weight = 9112.549| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.10 r_work: 0.3449 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1008 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 : 7.069 59.489 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 0.04732 ( 379) hydrogen bonds : angle 4.60495 ( 1056) SS BOND : bond 0.00393 ( 2) SS BOND : angle 1.12664 ( 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 : 0.936 Fit side-chains REVERT: C 212 ASP cc_start: 0.7633 (t70) cc_final: 0.7067 (t0) REVERT: C 215 GLU cc_start: 0.7820 (mp0) cc_final: 0.7333 (mp0) REVERT: C 255 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7968 (mp) REVERT: C 325 MET cc_start: 0.8622 (tpp) cc_final: 0.8299 (tpp) REVERT: F 115 ASN cc_start: 0.7815 (m-40) cc_final: 0.7598 (m-40) REVERT: F 198 ARG cc_start: 0.7267 (ttm110) cc_final: 0.6381 (mtm110) REVERT: F 261 ASP cc_start: 0.7561 (m-30) cc_final: 0.6493 (t0) REVERT: A 198 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7249 (tmm) REVERT: A 308 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7229 (mp0) outliers start: 60 outliers final: 32 residues processed: 155 average time/residue: 0.8818 time to fit residues: 148.4744 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 : 0.817 ------------------------------------------------------------------------------- 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: 0.9980 chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.206354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137745 restraints weight = 9187.514| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.58 r_work: 0.3488 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1301 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= 0.147 Angle : 0.623 9.877 11200 Z= 0.306 Chirality : 0.042 0.193 1289 Planarity : 0.004 0.053 1409 Dihedral : 6.046 58.665 1142 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 7.29 % Allowed : 26.27 % 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: 0.29 (0.26), residues: 1017 helix: 1.93 (0.29), residues: 347 sheet: 0.00 (0.32), residues: 250 loop : -1.19 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 105 HIS 0.004 0.001 HIS C 183 PHE 0.022 0.001 PHE C 199 TYR 0.015 0.002 TYR R 294 ARG 0.004 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 379) hydrogen bonds : angle 4.44238 ( 1056) SS BOND : bond 0.00382 ( 2) SS BOND : angle 1.04945 ( 4) covalent geometry : bond 0.00346 ( 8253) covalent geometry : angle 0.62277 (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 172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 109 time to evaluate : 0.786 Fit side-chains REVERT: C 212 ASP cc_start: 0.7587 (t70) cc_final: 0.7066 (t0) REVERT: C 215 GLU cc_start: 0.7881 (mp0) cc_final: 0.7324 (mp0) REVERT: C 217 MET cc_start: 0.7491 (ppp) cc_final: 0.7175 (pmt) REVERT: C 325 MET cc_start: 0.8552 (tpp) cc_final: 0.8228 (tpp) REVERT: E 21 MET cc_start: 0.7066 (mpp) cc_final: 0.6641 (mpp) REVERT: F 131 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7116 (tpp) REVERT: F 230 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7477 (ptp) REVERT: F 261 ASP cc_start: 0.7564 (m-30) cc_final: 0.6540 (t0) REVERT: R 181 GLN cc_start: 0.4206 (OUTLIER) cc_final: 0.3778 (mm-40) REVERT: A 198 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7168 (tmm) REVERT: A 216 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: A 308 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7214 (mp0) outliers start: 63 outliers final: 28 residues processed: 154 average time/residue: 0.7540 time to fit residues: 126.6590 Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 200 VAL 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 317 CYS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 131 MET 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 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 22 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 340 THR 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: 9.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 92 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 0.0670 chunk 8 optimal weight: 0.9980 overall best weight: 0.6096 ------------------------------------------------------------------------------- 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 A 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.208916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145568 restraints weight = 9130.503| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.67 r_work: 0.3517 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1550 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 : 0.595 11.872 11200 Z= 0.281 Chirality : 0.041 0.155 1289 Planarity : 0.004 0.051 1409 Dihedral : 5.402 58.309 1137 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 6.25 % Allowed : 27.66 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1017 helix: 2.02 (0.29), residues: 346 sheet: 0.16 (0.33), residues: 235 loop : -1.12 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 105 HIS 0.003 0.001 HIS A 195 PHE 0.021 0.001 PHE R 306 TYR 0.012 0.001 TYR F 228 ARG 0.008 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 379) hydrogen bonds : angle 4.25789 ( 1056) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.69082 ( 4) covalent geometry : bond 0.00225 ( 8253) covalent geometry : angle 0.59458 (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 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 114 time to evaluate : 0.813 Fit side-chains REVERT: C 212 ASP cc_start: 0.7473 (t70) cc_final: 0.7042 (t0) REVERT: C 215 GLU cc_start: 0.7887 (mp0) cc_final: 0.7462 (mp0) REVERT: C 217 MET cc_start: 0.7421 (ppp) cc_final: 0.7135 (pmt) REVERT: C 325 MET cc_start: 0.8541 (tpp) cc_final: 0.8163 (tpp) REVERT: F 115 ASN cc_start: 0.7899 (m-40) cc_final: 0.7662 (m-40) REVERT: F 131 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7057 (tpp) REVERT: F 198 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6305 (mtm110) REVERT: F 230 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7489 (ptp) REVERT: F 261 ASP cc_start: 0.7532 (m-30) cc_final: 0.6516 (t0) REVERT: F 273 TYR cc_start: 0.5703 (OUTLIER) cc_final: 0.5170 (t80) REVERT: A 198 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7212 (tmm) REVERT: A 308 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7078 (mp0) outliers start: 54 outliers final: 26 residues processed: 152 average time/residue: 0.8299 time to fit residues: 136.7102 Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 200 VAL 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 131 MET 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 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 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 329 THR 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: 3.9990 chunk 97 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN ** 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 = 0.4402 r_free = 0.4402 target = 0.207478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.139588 restraints weight = 9045.532| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.54 r_work: 0.3512 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1659 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 : 0.615 13.666 11200 Z= 0.293 Chirality : 0.041 0.165 1289 Planarity : 0.004 0.051 1409 Dihedral : 5.240 58.762 1134 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 7.06 % Allowed : 26.74 % Favored : 66.20 % 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: 0.36 (0.26), residues: 1017 helix: 1.98 (0.29), residues: 345 sheet: 0.11 (0.32), residues: 248 loop : -1.16 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 105 HIS 0.003 0.001 HIS F 73 PHE 0.017 0.001 PHE C 199 TYR 0.015 0.001 TYR R 294 ARG 0.006 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 379) hydrogen bonds : angle 4.24853 ( 1056) SS BOND : bond 0.00308 ( 2) SS BOND : angle 0.72735 ( 4) covalent geometry : bond 0.00279 ( 8253) covalent geometry : angle 0.61485 (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 165 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 104 time to evaluate : 0.875 Fit side-chains REVERT: C 134 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7737 (ptt-90) REVERT: C 212 ASP cc_start: 0.7425 (t70) cc_final: 0.7068 (t0) REVERT: C 215 GLU cc_start: 0.7930 (mp0) cc_final: 0.7566 (mp0) REVERT: C 217 MET cc_start: 0.7464 (ppp) cc_final: 0.7157 (pmt) REVERT: C 325 MET cc_start: 0.8539 (tpp) cc_final: 0.8148 (tpp) REVERT: E 21 MET cc_start: 0.6890 (mpp) cc_final: 0.6518 (mpp) REVERT: F 131 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7468 (tpp) REVERT: F 230 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7514 (ptp) REVERT: F 261 ASP cc_start: 0.7564 (m-30) cc_final: 0.6574 (t0) REVERT: F 273 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.5296 (t80) REVERT: A 195 HIS cc_start: 0.6163 (OUTLIER) cc_final: 0.5918 (t-170) REVERT: A 198 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7169 (tmm) REVERT: A 308 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7080 (mp0) outliers start: 61 outliers final: 34 residues processed: 146 average time/residue: 0.8066 time to fit residues: 128.0559 Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 61 MET 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 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 131 MET 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 118 LEU Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 135 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 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 329 THR 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: 0.2980 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.209049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.138982 restraints weight = 9272.380| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.67 r_work: 0.3532 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1836 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= 0.106 Angle : 0.599 10.713 11200 Z= 0.282 Chirality : 0.041 0.151 1289 Planarity : 0.004 0.052 1409 Dihedral : 4.984 59.229 1132 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.64 % Rotamer: Outliers : 6.37 % Allowed : 28.12 % Favored : 65.51 % 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: 0.41 (0.26), residues: 1017 helix: 1.98 (0.29), residues: 346 sheet: 0.17 (0.33), residues: 237 loop : -1.09 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 105 HIS 0.002 0.001 HIS F 73 PHE 0.017 0.001 PHE R 104 TYR 0.015 0.001 TYR R 294 ARG 0.010 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 379) hydrogen bonds : angle 4.19276 ( 1056) SS BOND : bond 0.00226 ( 2) SS BOND : angle 0.65739 ( 4) covalent geometry : bond 0.00236 ( 8253) covalent geometry : angle 0.59905 (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 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 113 time to evaluate : 0.810 Fit side-chains REVERT: C 134 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7729 (ptt-90) REVERT: C 212 ASP cc_start: 0.7383 (t70) cc_final: 0.7084 (t0) REVERT: C 215 GLU cc_start: 0.7933 (mp0) cc_final: 0.7560 (mp0) REVERT: C 217 MET cc_start: 0.7436 (ppp) cc_final: 0.7126 (pmt) REVERT: C 325 MET cc_start: 0.8499 (tpp) cc_final: 0.8109 (tpp) REVERT: E 21 MET cc_start: 0.6948 (mpp) cc_final: 0.6529 (mpp) REVERT: F 198 ARG cc_start: 0.7130 (ttm110) cc_final: 0.6504 (mtp85) REVERT: F 230 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7525 (ptp) REVERT: F 253 THR cc_start: 0.8308 (m) cc_final: 0.8085 (p) REVERT: F 261 ASP cc_start: 0.7687 (m-30) cc_final: 0.6545 (t0) REVERT: F 273 TYR cc_start: 0.5622 (OUTLIER) cc_final: 0.5092 (t80) REVERT: R 105 TRP cc_start: 0.5359 (t60) cc_final: 0.5133 (t60) REVERT: R 158 LEU cc_start: 0.4872 (pp) cc_final: 0.4327 (mt) REVERT: A 195 HIS cc_start: 0.6156 (OUTLIER) cc_final: 0.5882 (t-170) REVERT: A 198 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7335 (tmm) REVERT: A 308 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7168 (mp0) outliers start: 55 outliers final: 29 residues processed: 151 average time/residue: 0.9181 time to fit residues: 149.7458 Evaluate side-chains 141 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 61 MET 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 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 331 SER 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 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 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 329 THR 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: 0.6980 chunk 22 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 = 0.4414 r_free = 0.4414 target = 0.208906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.141296 restraints weight = 9131.798| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.78 r_work: 0.3512 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8255 Z= 0.109 Angle : 0.626 13.381 11200 Z= 0.294 Chirality : 0.041 0.146 1289 Planarity : 0.004 0.051 1409 Dihedral : 4.841 59.718 1131 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.35 % Rotamer: Outliers : 6.60 % Allowed : 28.24 % Favored : 65.16 % 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: 0.42 (0.26), residues: 1017 helix: 1.98 (0.29), residues: 345 sheet: 0.21 (0.33), residues: 237 loop : -1.09 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 105 HIS 0.002 0.001 HIS F 73 PHE 0.014 0.001 PHE R 95 TYR 0.020 0.001 TYR R 294 ARG 0.009 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 379) hydrogen bonds : angle 4.19202 ( 1056) SS BOND : bond 0.00258 ( 2) SS BOND : angle 0.60966 ( 4) covalent geometry : bond 0.00246 ( 8253) covalent geometry : angle 0.62598 (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 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 106 time to evaluate : 0.863 Fit side-chains REVERT: C 134 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7764 (ptt-90) REVERT: C 212 ASP cc_start: 0.7375 (t70) cc_final: 0.7035 (t0) REVERT: C 215 GLU cc_start: 0.7897 (mp0) cc_final: 0.7491 (mp0) REVERT: C 217 MET cc_start: 0.7399 (ppp) cc_final: 0.7089 (pmt) REVERT: C 325 MET cc_start: 0.8526 (tpp) cc_final: 0.8106 (tpp) REVERT: E 21 MET cc_start: 0.6971 (mpp) cc_final: 0.6565 (mpp) REVERT: F 115 ASN cc_start: 0.7866 (m-40) cc_final: 0.7626 (m-40) REVERT: F 198 ARG cc_start: 0.7079 (ttm110) cc_final: 0.6438 (mtp85) REVERT: F 230 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7577 (ptp) REVERT: F 261 ASP cc_start: 0.7649 (m-30) cc_final: 0.6505 (t0) REVERT: F 273 TYR cc_start: 0.5594 (OUTLIER) cc_final: 0.5094 (t80) REVERT: R 158 LEU cc_start: 0.4829 (pp) cc_final: 0.4266 (mt) REVERT: A 195 HIS cc_start: 0.6149 (OUTLIER) cc_final: 0.5876 (t-170) REVERT: A 198 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7287 (tmm) REVERT: A 308 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7161 (mp0) outliers start: 57 outliers final: 32 residues processed: 147 average time/residue: 0.8364 time to fit residues: 133.6480 Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 61 MET 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 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 37 LEU 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 196 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 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 329 THR 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: 3.9990 chunk 91 optimal weight: 0.0770 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.205802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143154 restraints weight = 9204.524| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.65 r_work: 0.3455 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8255 Z= 0.158 Angle : 0.672 12.167 11200 Z= 0.321 Chirality : 0.042 0.189 1289 Planarity : 0.004 0.052 1409 Dihedral : 5.033 59.004 1131 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 6.94 % Allowed : 28.47 % 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: 0.34 (0.26), residues: 1017 helix: 1.94 (0.28), residues: 345 sheet: 0.20 (0.32), residues: 248 loop : -1.24 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 105 HIS 0.004 0.001 HIS F 73 PHE 0.015 0.001 PHE R 95 TYR 0.024 0.002 TYR R 294 ARG 0.007 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 379) hydrogen bonds : angle 4.34136 ( 1056) SS BOND : bond 0.00529 ( 2) SS BOND : angle 0.79447 ( 4) covalent geometry : bond 0.00378 ( 8253) covalent geometry : angle 0.67232 (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 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 101 time to evaluate : 0.809 Fit side-chains REVERT: C 212 ASP cc_start: 0.7401 (t70) cc_final: 0.7047 (t0) REVERT: C 215 GLU cc_start: 0.7947 (mp0) cc_final: 0.7486 (mp0) REVERT: C 217 MET cc_start: 0.7501 (ppp) cc_final: 0.7131 (pmt) REVERT: C 325 MET cc_start: 0.8577 (tpp) cc_final: 0.8223 (tpp) REVERT: E 21 MET cc_start: 0.7050 (mpp) cc_final: 0.6758 (mpp) REVERT: F 230 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7647 (ptp) REVERT: F 261 ASP cc_start: 0.7649 (m-30) cc_final: 0.6532 (t0) REVERT: F 273 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.5478 (t80) REVERT: R 158 LEU cc_start: 0.4863 (pp) cc_final: 0.4289 (mt) REVERT: A 195 HIS cc_start: 0.6235 (OUTLIER) cc_final: 0.6013 (t-90) REVERT: A 198 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7222 (tmm) REVERT: A 216 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: A 308 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7089 (mp0) outliers start: 60 outliers final: 34 residues processed: 144 average time/residue: 0.8167 time to fit residues: 127.8933 Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 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 61 MET 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 103 CYS 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 98 THR 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 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 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 216 GLU Chi-restraints excluded: chain A residue 308 GLU 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: 1.9990 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 60 optimal weight: 0.0770 chunk 2 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- 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 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.207024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139529 restraints weight = 9376.246| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.26 r_work: 0.3456 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8255 Z= 0.140 Angle : 0.665 13.449 11200 Z= 0.316 Chirality : 0.042 0.183 1289 Planarity : 0.004 0.054 1409 Dihedral : 4.967 58.922 1131 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 5.67 % Allowed : 29.98 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.28), residues: 347 sheet: 0.15 (0.32), residues: 250 loop : -1.28 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 105 HIS 0.003 0.001 HIS F 73 PHE 0.032 0.001 PHE R 315 TYR 0.021 0.002 TYR R 294 ARG 0.013 0.001 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 379) hydrogen bonds : angle 4.27922 ( 1056) SS BOND : bond 0.00364 ( 2) SS BOND : angle 0.70743 ( 4) covalent geometry : bond 0.00330 ( 8253) covalent geometry : angle 0.66536 (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 151 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 102 time to evaluate : 0.826 Fit side-chains REVERT: C 212 ASP cc_start: 0.7465 (t70) cc_final: 0.7106 (t0) REVERT: C 215 GLU cc_start: 0.7986 (mp0) cc_final: 0.7545 (mp0) REVERT: C 217 MET cc_start: 0.7630 (ppp) cc_final: 0.7287 (pmt) REVERT: C 270 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7893 (mp) REVERT: C 325 MET cc_start: 0.8593 (tpp) cc_final: 0.8235 (tpp) REVERT: F 198 ARG cc_start: 0.7114 (ttm110) cc_final: 0.6452 (mtp85) REVERT: F 230 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7644 (ptp) REVERT: F 261 ASP cc_start: 0.7624 (m-30) cc_final: 0.6537 (t0) REVERT: F 273 TYR cc_start: 0.6058 (OUTLIER) cc_final: 0.5428 (t80) REVERT: R 136 ASP cc_start: 0.6893 (t0) cc_final: 0.6598 (t0) REVERT: R 158 LEU cc_start: 0.4755 (pp) cc_final: 0.4209 (mt) REVERT: A 195 HIS cc_start: 0.6149 (OUTLIER) cc_final: 0.5918 (t-90) REVERT: A 198 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7358 (tmm) REVERT: A 216 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: A 308 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7115 (mp0) outliers start: 49 outliers final: 34 residues processed: 139 average time/residue: 0.8362 time to fit residues: 125.9639 Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 61 MET 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 103 CYS 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 270 ILE 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 196 LEU Chi-restraints excluded: chain R residue 203 ILE 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 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 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 216 GLU Chi-restraints excluded: chain A residue 308 GLU 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 90 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 81 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 = 0.4368 r_free = 0.4368 target = 0.203794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135694 restraints weight = 9187.261| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.99 r_work: 0.3415 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8255 Z= 0.238 Angle : 0.740 13.063 11200 Z= 0.359 Chirality : 0.045 0.230 1289 Planarity : 0.005 0.066 1409 Dihedral : 5.235 57.276 1131 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 6.02 % Allowed : 29.75 % 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: 0.13 (0.26), residues: 1017 helix: 1.80 (0.28), residues: 347 sheet: -0.04 (0.32), residues: 258 loop : -1.34 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 105 HIS 0.007 0.001 HIS F 73 PHE 0.052 0.002 PHE R 315 TYR 0.027 0.002 TYR R 294 ARG 0.011 0.001 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 379) hydrogen bonds : angle 4.43659 ( 1056) SS BOND : bond 0.00559 ( 2) SS BOND : angle 1.23433 ( 4) covalent geometry : bond 0.00581 ( 8253) covalent geometry : angle 0.73938 (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 156 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 104 time to evaluate : 0.824 Fit side-chains REVERT: C 212 ASP cc_start: 0.7549 (t70) cc_final: 0.7132 (t0) REVERT: C 215 GLU cc_start: 0.7989 (mp0) cc_final: 0.7413 (mp0) REVERT: C 217 MET cc_start: 0.7669 (ppp) cc_final: 0.7318 (pmt) REVERT: C 325 MET cc_start: 0.8658 (tpp) cc_final: 0.8333 (tpp) REVERT: F 198 ARG cc_start: 0.7136 (ttm110) cc_final: 0.6274 (mtm110) REVERT: F 230 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7681 (ptp) REVERT: F 261 ASP cc_start: 0.7622 (m-30) cc_final: 0.6524 (t0) REVERT: F 273 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.5855 (t80) REVERT: R 158 LEU cc_start: 0.4772 (pp) cc_final: 0.4219 (mt) REVERT: A 195 HIS cc_start: 0.6145 (OUTLIER) cc_final: 0.5921 (t-90) REVERT: A 198 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7070 (tmm) REVERT: A 216 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: A 308 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7150 (mp0) outliers start: 52 outliers final: 32 residues processed: 141 average time/residue: 0.8512 time to fit residues: 130.0352 Evaluate side-chains 139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 103 CYS 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 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 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 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 216 GLU 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: 4.9990 chunk 58 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.205919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135851 restraints weight = 9278.772| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.22 r_work: 0.3445 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8255 Z= 0.156 Angle : 0.691 12.501 11200 Z= 0.329 Chirality : 0.043 0.203 1289 Planarity : 0.004 0.058 1409 Dihedral : 5.083 57.748 1131 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.85 % Favored : 97.05 % Rotamer: Outliers : 5.44 % Allowed : 30.56 % 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: 0.16 (0.26), residues: 1017 helix: 1.84 (0.28), residues: 347 sheet: 0.03 (0.32), residues: 250 loop : -1.35 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 105 HIS 0.004 0.001 HIS F 73 PHE 0.027 0.001 PHE R 315 TYR 0.023 0.002 TYR R 294 ARG 0.011 0.000 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 379) hydrogen bonds : angle 4.33096 ( 1056) SS BOND : bond 0.00439 ( 2) SS BOND : angle 0.93494 ( 4) covalent geometry : bond 0.00371 ( 8253) covalent geometry : angle 0.69089 (11196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6023.46 seconds wall clock time: 104 minutes 19.85 seconds (6259.85 seconds total)