Starting phenix.real_space_refine on Sat May 10 12:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8geb_29964/05_2025/8geb_29964.cif Found real_map, /net/cci-nas-00/data/ceres_data/8geb_29964/05_2025/8geb_29964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8geb_29964/05_2025/8geb_29964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8geb_29964/05_2025/8geb_29964.map" model { file = "/net/cci-nas-00/data/ceres_data/8geb_29964/05_2025/8geb_29964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8geb_29964/05_2025/8geb_29964.cif" } resolution = 3.6 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= 0.028 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 36 5.16 5 C 4017 2.51 5 N 1091 2.21 5 O 1079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6223 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1650 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 3 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 198 Chain: "B" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2301 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 6, 'ASP:plan': 19} Unresolved non-hydrogen planarities: 158 Chain: "G" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 319 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1938 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.79 Number of scatterers: 6223 At special positions: 0 Unit cell: (68.9, 98.58, 127.2, 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 36 16.00 O 1079 8.00 N 1091 7.00 C 4017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 1.45 Conformation dependent library (CDL) restraints added in 889.3 milliseconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 47.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.420A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.043A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.735A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.641A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.522A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.546A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.683A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET R 40 " --> pdb=" O MET R 36 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.895A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix removed outlier: 3.506A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 298 removed outlier: 4.111A pdb=" N CYS R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.169A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 Processing helix chain 'R' and resid 321 through 327 removed outlier: 3.611A pdb=" N ILE R 325 " --> pdb=" O PHE R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 6.848A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50 removed outlier: 5.914A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 329 " --> pdb=" O LYS B 337 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.102A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.507A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.523A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.807A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.790A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.272A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1987 1.34 - 1.45: 886 1.45 - 1.57: 3436 1.57 - 1.69: 1 1.69 - 1.81: 48 Bond restraints: 6358 Sorted by residual: bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.575 -0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.441 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" CA ALA B 73 " pdb=" CB ALA B 73 " ideal model delta sigma weight residual 1.532 1.496 0.035 1.82e-02 3.02e+03 3.79e+00 ... (remaining 6353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 8572 1.70 - 3.41: 121 3.41 - 5.11: 13 5.11 - 6.82: 6 6.82 - 8.52: 2 Bond angle restraints: 8714 Sorted by residual: angle pdb=" N ILE B 269 " pdb=" CA ILE B 269 " pdb=" C ILE B 269 " ideal model delta sigma weight residual 109.34 117.26 -7.92 2.08e+00 2.31e-01 1.45e+01 angle pdb=" CB MET B 188 " pdb=" CG MET B 188 " pdb=" SD MET B 188 " ideal model delta sigma weight residual 112.70 104.18 8.52 3.00e+00 1.11e-01 8.06e+00 angle pdb=" N CYS B 271 " pdb=" CA CYS B 271 " pdb=" C CYS B 271 " ideal model delta sigma weight residual 110.59 114.37 -3.78 1.45e+00 4.76e-01 6.79e+00 angle pdb=" N SER B 74 " pdb=" CA SER B 74 " pdb=" C SER B 74 " ideal model delta sigma weight residual 109.85 113.95 -4.10 1.58e+00 4.01e-01 6.73e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 121.14 116.74 4.40 1.75e+00 3.27e-01 6.31e+00 ... (remaining 8709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 3352 16.71 - 33.41: 249 33.41 - 50.12: 45 50.12 - 66.82: 9 66.82 - 83.53: 2 Dihedral angle restraints: 3657 sinusoidal: 1051 harmonic: 2606 Sorted by residual: dihedral pdb=" CA ILE R 298 " pdb=" C ILE R 298 " pdb=" N GLN R 299 " pdb=" CA GLN R 299 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA MET B 262 " pdb=" C MET B 262 " pdb=" N THR B 263 " pdb=" CA THR B 263 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 650 0.030 - 0.060: 273 0.060 - 0.090: 84 0.090 - 0.121: 41 0.121 - 0.151: 2 Chirality restraints: 1050 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1047 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO R 323 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO B 194 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 321 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.015 5.00e-02 4.00e+02 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2190 2.85 - 3.36: 5967 3.36 - 3.87: 10203 3.87 - 4.39: 10707 4.39 - 4.90: 19725 Nonbonded interactions: 48792 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.333 3.040 nonbonded pdb=" OG SER B 279 " pdb=" OD2 ASP G 48 " model vdw 2.336 3.040 nonbonded pdb=" NH1 ARG B 137 " pdb=" O ILE B 171 " model vdw 2.373 3.120 nonbonded pdb=" OD1 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.375 3.040 nonbonded pdb=" O ARG A 283 " pdb=" NH1 ARG A 356 " model vdw 2.380 3.120 ... (remaining 48787 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 0.052 6359 Z= 0.163 Angle : 0.520 8.519 8716 Z= 0.275 Chirality : 0.040 0.151 1050 Planarity : 0.003 0.044 1106 Dihedral : 12.499 83.527 1960 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 1.44 (0.29), residues: 875 helix: 2.72 (0.26), residues: 396 sheet: 0.15 (0.41), residues: 162 loop : -0.95 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 281 HIS 0.006 0.001 HIS B 266 PHE 0.007 0.001 PHE A 212 TYR 0.011 0.001 TYR R 199 ARG 0.007 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.13781 ( 373) hydrogen bonds : angle 5.93691 ( 1086) SS BOND : bond 0.00379 ( 1) SS BOND : angle 0.28311 ( 2) covalent geometry : bond 0.00333 ( 6358) covalent geometry : angle 0.52000 ( 8714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.748 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1383 time to fit residues: 16.9501 Evaluate side-chains 64 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108329 restraints weight = 10259.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111412 restraints weight = 5868.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113424 restraints weight = 4037.557| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6359 Z= 0.144 Angle : 0.466 5.480 8716 Z= 0.253 Chirality : 0.040 0.143 1050 Planarity : 0.003 0.043 1106 Dihedral : 4.403 30.647 959 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.20 % Allowed : 10.00 % Favored : 88.80 % 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: 1.48 (0.29), residues: 875 helix: 2.75 (0.26), residues: 399 sheet: 0.19 (0.40), residues: 161 loop : -0.97 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 PHE 0.009 0.001 PHE B 235 TYR 0.013 0.001 TYR R 199 ARG 0.008 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 373) hydrogen bonds : angle 4.58610 ( 1086) SS BOND : bond 0.00421 ( 1) SS BOND : angle 0.36518 ( 2) covalent geometry : bond 0.00330 ( 6358) covalent geometry : angle 0.46589 ( 8714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.715 Fit side-chains REVERT: B 258 ASP cc_start: 0.8260 (t70) cc_final: 0.7913 (t0) REVERT: R 58 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8307 (mp) outliers start: 6 outliers final: 5 residues processed: 76 average time/residue: 0.1306 time to fit residues: 14.8147 Evaluate side-chains 71 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 78 optimal weight: 0.0670 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN R 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111206 restraints weight = 10690.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114149 restraints weight = 6292.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116166 restraints weight = 4357.956| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6359 Z= 0.118 Angle : 0.429 5.415 8716 Z= 0.233 Chirality : 0.039 0.142 1050 Planarity : 0.003 0.041 1106 Dihedral : 4.159 27.794 959 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.20 % Allowed : 13.40 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.29), residues: 875 helix: 2.79 (0.26), residues: 399 sheet: 0.25 (0.40), residues: 164 loop : -0.95 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS B 225 PHE 0.008 0.001 PHE A 212 TYR 0.012 0.001 TYR R 199 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 373) hydrogen bonds : angle 4.26798 ( 1086) SS BOND : bond 0.00338 ( 1) SS BOND : angle 0.29305 ( 2) covalent geometry : bond 0.00271 ( 6358) covalent geometry : angle 0.42877 ( 8714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.675 Fit side-chains REVERT: B 188 MET cc_start: 0.7785 (mmm) cc_final: 0.7465 (mmt) REVERT: B 233 CYS cc_start: 0.8202 (t) cc_final: 0.7877 (t) REVERT: B 258 ASP cc_start: 0.8174 (t70) cc_final: 0.7832 (t0) REVERT: R 58 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8313 (mp) outliers start: 11 outliers final: 8 residues processed: 79 average time/residue: 0.1183 time to fit residues: 14.2896 Evaluate side-chains 77 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108922 restraints weight = 10801.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111724 restraints weight = 6434.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113588 restraints weight = 4524.968| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6359 Z= 0.145 Angle : 0.450 5.502 8716 Z= 0.245 Chirality : 0.040 0.186 1050 Planarity : 0.003 0.042 1106 Dihedral : 4.157 28.152 959 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.60 % Allowed : 15.20 % Favored : 82.20 % 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: 1.53 (0.29), residues: 875 helix: 2.87 (0.25), residues: 393 sheet: 0.12 (0.40), residues: 164 loop : -0.93 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.010 0.001 PHE B 235 TYR 0.013 0.001 TYR R 199 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 373) hydrogen bonds : angle 4.19452 ( 1086) SS BOND : bond 0.00477 ( 1) SS BOND : angle 0.43939 ( 2) covalent geometry : bond 0.00340 ( 6358) covalent geometry : angle 0.45046 ( 8714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.809 Fit side-chains REVERT: B 233 CYS cc_start: 0.8221 (t) cc_final: 0.7921 (t) REVERT: B 258 ASP cc_start: 0.8199 (t70) cc_final: 0.7932 (t0) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.1220 time to fit residues: 14.1311 Evaluate side-chains 76 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106866 restraints weight = 10448.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109946 restraints weight = 5967.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112078 restraints weight = 4098.861| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6359 Z= 0.133 Angle : 0.446 5.895 8716 Z= 0.241 Chirality : 0.039 0.137 1050 Planarity : 0.003 0.040 1106 Dihedral : 4.115 28.509 959 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.60 % Allowed : 16.60 % Favored : 80.80 % 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: 1.52 (0.29), residues: 875 helix: 2.88 (0.25), residues: 393 sheet: 0.06 (0.40), residues: 164 loop : -0.93 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.009 0.001 PHE A 212 TYR 0.013 0.001 TYR R 199 ARG 0.004 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 373) hydrogen bonds : angle 4.08728 ( 1086) SS BOND : bond 0.00396 ( 1) SS BOND : angle 0.38564 ( 2) covalent geometry : bond 0.00311 ( 6358) covalent geometry : angle 0.44614 ( 8714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.650 Fit side-chains REVERT: B 82 TRP cc_start: 0.8136 (OUTLIER) cc_final: 0.7368 (m-90) REVERT: B 233 CYS cc_start: 0.8208 (t) cc_final: 0.7927 (t) REVERT: B 258 ASP cc_start: 0.8185 (t70) cc_final: 0.7932 (t0) outliers start: 13 outliers final: 11 residues processed: 82 average time/residue: 0.1329 time to fit residues: 16.3667 Evaluate side-chains 80 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 7 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.0570 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 29 optimal weight: 0.0980 chunk 78 optimal weight: 0.3980 overall best weight: 0.1656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111996 restraints weight = 10221.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115138 restraints weight = 5779.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117309 restraints weight = 3940.902| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6359 Z= 0.084 Angle : 0.433 10.708 8716 Z= 0.225 Chirality : 0.038 0.131 1050 Planarity : 0.003 0.036 1106 Dihedral : 3.846 28.531 959 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.20 % Allowed : 17.60 % Favored : 80.20 % 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: 1.75 (0.29), residues: 875 helix: 3.09 (0.25), residues: 393 sheet: 0.27 (0.40), residues: 158 loop : -0.89 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.000 HIS B 311 PHE 0.010 0.001 PHE A 212 TYR 0.010 0.001 TYR R 199 ARG 0.003 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 373) hydrogen bonds : angle 3.76599 ( 1086) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.17624 ( 2) covalent geometry : bond 0.00177 ( 6358) covalent geometry : angle 0.43328 ( 8714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.809 Fit side-chains REVERT: B 233 CYS cc_start: 0.8101 (t) cc_final: 0.7776 (t) REVERT: B 234 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8355 (t80) REVERT: B 258 ASP cc_start: 0.8100 (t70) cc_final: 0.7854 (t0) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.1289 time to fit residues: 16.5502 Evaluate side-chains 80 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 0.0170 chunk 37 optimal weight: 0.0370 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.128510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110726 restraints weight = 10377.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113870 restraints weight = 5973.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115983 restraints weight = 4088.279| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6359 Z= 0.099 Angle : 0.436 8.105 8716 Z= 0.230 Chirality : 0.039 0.135 1050 Planarity : 0.003 0.037 1106 Dihedral : 3.787 27.529 959 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.40 % Allowed : 16.80 % Favored : 79.80 % 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: 1.75 (0.29), residues: 875 helix: 3.10 (0.25), residues: 393 sheet: 0.18 (0.40), residues: 160 loop : -0.86 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.002 0.001 HIS B 311 PHE 0.007 0.001 PHE A 212 TYR 0.011 0.001 TYR R 199 ARG 0.005 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 373) hydrogen bonds : angle 3.73355 ( 1086) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.14815 ( 2) covalent geometry : bond 0.00223 ( 6358) covalent geometry : angle 0.43609 ( 8714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.732 Fit side-chains REVERT: B 82 TRP cc_start: 0.8084 (OUTLIER) cc_final: 0.7220 (m-10) REVERT: B 233 CYS cc_start: 0.8125 (t) cc_final: 0.7809 (t) REVERT: B 234 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8372 (t80) REVERT: B 258 ASP cc_start: 0.8127 (t70) cc_final: 0.7857 (t0) outliers start: 17 outliers final: 12 residues processed: 85 average time/residue: 0.1282 time to fit residues: 16.3756 Evaluate side-chains 83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 76 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112715 restraints weight = 10660.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115558 restraints weight = 6259.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117353 restraints weight = 4368.726| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6359 Z= 0.103 Angle : 0.441 8.203 8716 Z= 0.232 Chirality : 0.039 0.135 1050 Planarity : 0.003 0.037 1106 Dihedral : 3.804 28.320 959 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.40 % Allowed : 16.20 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.29), residues: 875 helix: 3.03 (0.26), residues: 399 sheet: 0.10 (0.40), residues: 160 loop : -0.85 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 281 HIS 0.002 0.001 HIS B 311 PHE 0.009 0.001 PHE R 321 TYR 0.011 0.001 TYR R 199 ARG 0.004 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 373) hydrogen bonds : angle 3.71168 ( 1086) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.19976 ( 2) covalent geometry : bond 0.00232 ( 6358) covalent geometry : angle 0.44094 ( 8714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.786 Fit side-chains REVERT: B 82 TRP cc_start: 0.8035 (OUTLIER) cc_final: 0.7192 (m-10) REVERT: B 233 CYS cc_start: 0.8126 (t) cc_final: 0.7836 (t) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 258 ASP cc_start: 0.8138 (t70) cc_final: 0.7866 (t0) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.1153 time to fit residues: 14.6916 Evaluate side-chains 80 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106600 restraints weight = 10786.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109303 restraints weight = 6455.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111189 restraints weight = 4592.458| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6359 Z= 0.201 Angle : 0.532 7.467 8716 Z= 0.282 Chirality : 0.041 0.135 1050 Planarity : 0.003 0.038 1106 Dihedral : 4.211 29.884 959 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.80 % Allowed : 18.20 % Favored : 79.00 % 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: 1.42 (0.29), residues: 875 helix: 2.72 (0.25), residues: 399 sheet: -0.08 (0.39), residues: 169 loop : -0.90 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 281 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE B 235 TYR 0.016 0.002 TYR R 199 ARG 0.005 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 373) hydrogen bonds : angle 4.12349 ( 1086) SS BOND : bond 0.00720 ( 1) SS BOND : angle 0.81957 ( 2) covalent geometry : bond 0.00479 ( 6358) covalent geometry : angle 0.53176 ( 8714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.658 Fit side-chains REVERT: B 82 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.7567 (m-10) REVERT: B 258 ASP cc_start: 0.8282 (t70) cc_final: 0.8053 (t0) REVERT: R 82 MET cc_start: 0.7520 (ttp) cc_final: 0.7276 (ttp) REVERT: R 316 TYR cc_start: 0.8289 (m-10) cc_final: 0.7852 (m-10) outliers start: 14 outliers final: 12 residues processed: 81 average time/residue: 0.1114 time to fit residues: 13.9915 Evaluate side-chains 79 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110276 restraints weight = 10663.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113089 restraints weight = 6254.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115092 restraints weight = 4338.830| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6359 Z= 0.106 Angle : 0.460 7.976 8716 Z= 0.242 Chirality : 0.039 0.231 1050 Planarity : 0.003 0.035 1106 Dihedral : 4.012 29.427 959 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.40 % Allowed : 19.40 % Favored : 78.20 % 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: 1.53 (0.29), residues: 875 helix: 2.97 (0.25), residues: 393 sheet: -0.20 (0.39), residues: 169 loop : -0.89 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 281 HIS 0.002 0.001 HIS B 311 PHE 0.010 0.001 PHE A 212 TYR 0.012 0.001 TYR R 199 ARG 0.004 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 373) hydrogen bonds : angle 3.87450 ( 1086) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.29928 ( 2) covalent geometry : bond 0.00239 ( 6358) covalent geometry : angle 0.46021 ( 8714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.693 Fit side-chains REVERT: B 82 TRP cc_start: 0.8095 (OUTLIER) cc_final: 0.7393 (m-10) REVERT: B 258 ASP cc_start: 0.8247 (t70) cc_final: 0.8012 (t0) outliers start: 12 outliers final: 11 residues processed: 80 average time/residue: 0.1136 time to fit residues: 14.0925 Evaluate side-chains 82 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 0.0980 chunk 63 optimal weight: 0.2980 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111563 restraints weight = 10713.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114430 restraints weight = 6206.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116443 restraints weight = 4278.948| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6359 Z= 0.102 Angle : 0.450 7.926 8716 Z= 0.237 Chirality : 0.039 0.226 1050 Planarity : 0.003 0.035 1106 Dihedral : 3.875 28.585 959 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.60 % Allowed : 19.80 % Favored : 77.60 % 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: 1.59 (0.29), residues: 875 helix: 2.98 (0.25), residues: 399 sheet: -0.21 (0.39), residues: 167 loop : -0.85 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.002 0.001 HIS B 311 PHE 0.009 0.001 PHE A 212 TYR 0.012 0.001 TYR R 199 ARG 0.004 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.03135 ( 373) hydrogen bonds : angle 3.77125 ( 1086) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.14459 ( 2) covalent geometry : bond 0.00231 ( 6358) covalent geometry : angle 0.44956 ( 8714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1975.69 seconds wall clock time: 35 minutes 19.61 seconds (2119.61 seconds total)