Starting phenix.real_space_refine on Wed Mar 12 17:35:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6d_36001/03_2025/8j6d_36001.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6d_36001/03_2025/8j6d_36001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6d_36001/03_2025/8j6d_36001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6d_36001/03_2025/8j6d_36001.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6d_36001/03_2025/8j6d_36001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6d_36001/03_2025/8j6d_36001.cif" } resolution = 3.1 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= 0.005 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5197 2.51 5 N 1401 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8149 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1578 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2402 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2027 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 14, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Chain: "D" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 386 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1683 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 5.28, per 1000 atoms: 0.65 Number of scatterers: 8149 At special positions: 0 Unit cell: (85.1, 118.45, 123.05, 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 54 16.00 O 1497 8.00 N 1401 7.00 C 5197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.7% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.668A pdb=" N GLU A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.351A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.043A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.954A pdb=" N ALA A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.545A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 20 through 50 removed outlier: 3.847A pdb=" N VAL C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 55 through 85 removed outlier: 4.408A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 91 through 126 Proline residue: C 99 - end of helix removed outlier: 3.826A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 135 through 154 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 332 through 363 removed outlier: 3.738A pdb=" N THR C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 364 through 370 removed outlier: 6.842A pdb=" N ARG C 367 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS C 370 " --> pdb=" O ARG C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 403 removed outlier: 3.814A pdb=" N PHE C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 4.075A pdb=" N GLY C 397 " --> pdb=" O TYR C 393 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 398 " --> pdb=" O HIS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 436 removed outlier: 4.750A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 439 through 448 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 53 through 56 removed outlier: 4.273A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 3.561A pdb=" N ASP A 201 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.557A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.890A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.982A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.115A 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: 3.965A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.571A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.000A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.333A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.674A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.632A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 5.948A pdb=" N VAL H 147 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1248 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: 2.37 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1987 1.33 - 1.45: 1730 1.45 - 1.57: 4537 1.57 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 8325 Sorted by residual: bond pdb=" N ASP G 48 " pdb=" CA ASP G 48 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.06e-02 8.90e+03 7.36e+00 bond pdb=" C GLY C 439 " pdb=" O GLY C 439 " ideal model delta sigma weight residual 1.231 1.266 -0.035 1.33e-02 5.65e+03 6.94e+00 bond pdb=" N ARG D 69 " pdb=" CA ARG D 69 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.32e-02 5.74e+03 6.59e+00 bond pdb=" N THR C 331 " pdb=" CA THR C 331 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.90e-02 2.77e+03 6.33e+00 bond pdb=" C ARG C 443 " pdb=" O ARG C 443 " ideal model delta sigma weight residual 1.236 1.263 -0.027 1.15e-02 7.56e+03 5.44e+00 ... (remaining 8320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 11025 1.82 - 3.65: 272 3.65 - 5.47: 44 5.47 - 7.29: 9 7.29 - 9.11: 3 Bond angle restraints: 11353 Sorted by residual: angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 111.62 107.06 4.56 7.90e-01 1.60e+00 3.34e+01 angle pdb=" CA THR C 331 " pdb=" C THR C 331 " pdb=" N PRO C 332 " ideal model delta sigma weight residual 116.90 124.14 -7.24 1.50e+00 4.44e-01 2.33e+01 angle pdb=" C ARG D 69 " pdb=" CA ARG D 69 " pdb=" CB ARG D 69 " ideal model delta sigma weight residual 110.11 101.37 8.74 1.90e+00 2.77e-01 2.12e+01 angle pdb=" C ILE C 29 " pdb=" N LEU C 30 " pdb=" CA LEU C 30 " ideal model delta sigma weight residual 120.58 112.87 7.71 1.71e+00 3.42e-01 2.03e+01 angle pdb=" CA LEU C 438 " pdb=" C LEU C 438 " pdb=" N GLY C 439 " ideal model delta sigma weight residual 118.41 112.42 5.99 1.34e+00 5.57e-01 2.00e+01 ... (remaining 11348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 4414 16.10 - 32.20: 353 32.20 - 48.30: 73 48.30 - 64.40: 11 64.40 - 80.50: 3 Dihedral angle restraints: 4854 sinusoidal: 1616 harmonic: 3238 Sorted by residual: dihedral pdb=" CA GLN C 364 " pdb=" C GLN C 364 " pdb=" N ARG C 365 " pdb=" CA ARG C 365 " ideal model delta harmonic sigma weight residual 180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLU A 8 " pdb=" C GLU A 8 " pdb=" N GLU A 9 " pdb=" CA GLU A 9 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ASP A 218 " pdb=" C ASP A 218 " pdb=" N VAL A 219 " pdb=" CA VAL A 219 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 4851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1098 0.057 - 0.113: 200 0.113 - 0.170: 30 0.170 - 0.227: 0 0.227 - 0.283: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA THR C 331 " pdb=" N THR C 331 " pdb=" C THR C 331 " pdb=" CB THR C 331 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA PHE C 164 " pdb=" N PHE C 164 " pdb=" C PHE C 164 " pdb=" CB PHE C 164 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA ARG D 69 " pdb=" N ARG D 69 " pdb=" C ARG D 69 " pdb=" CB ARG D 69 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1326 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 438 " 0.015 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU C 438 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU C 438 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 439 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 98 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 99 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 235 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO H 236 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 236 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 236 " -0.026 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 188 2.69 - 3.24: 8683 3.24 - 3.79: 12850 3.79 - 4.35: 17444 4.35 - 4.90: 29179 Nonbonded interactions: 68344 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.209 3.040 nonbonded pdb=" O ASN B 268 " pdb=" OD1 ASN B 268 " model vdw 2.251 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 177 " model vdw 2.255 3.040 ... (remaining 68339 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: 1.870 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 : 0.004 0.048 8325 Z= 0.287 Angle : 0.730 9.114 11353 Z= 0.425 Chirality : 0.045 0.283 1329 Planarity : 0.005 0.052 1450 Dihedral : 12.635 80.495 2755 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.38 % Allowed : 11.93 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.02 (0.25), residues: 1103 helix: -0.39 (0.24), residues: 393 sheet: -0.52 (0.33), residues: 258 loop : -0.84 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 99 HIS 0.011 0.002 HIS B 311 PHE 0.018 0.002 PHE B 235 TYR 0.018 0.002 TYR C 393 ARG 0.011 0.001 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 174 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 145 TYR cc_start: 0.7754 (p90) cc_final: 0.7148 (p90) REVERT: C 90 TYR cc_start: 0.5293 (m-80) cc_final: 0.4851 (m-80) REVERT: C 412 THR cc_start: 0.7380 (m) cc_final: 0.6727 (m) REVERT: G 48 ASP cc_start: 0.7204 (t0) cc_final: 0.6950 (t0) REVERT: H 216 ILE cc_start: 0.8342 (mp) cc_final: 0.8108 (mt) outliers start: 3 outliers final: 3 residues processed: 176 average time/residue: 0.2280 time to fit residues: 52.6677 Evaluate side-chains 151 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain D residue 77 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.0010 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 86 optimal weight: 0.1980 chunk 33 optimal weight: 0.3980 chunk 52 optimal weight: 0.0170 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 0.1980 overall best weight: 0.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN B 32 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN H 39 GLN H 179 GLN H 183 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.129793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.112776 restraints weight = 17281.248| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.29 r_work: 0.3741 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8325 Z= 0.170 Angle : 0.625 11.733 11353 Z= 0.322 Chirality : 0.044 0.236 1329 Planarity : 0.004 0.052 1450 Dihedral : 5.281 56.404 1199 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.90 % Allowed : 12.44 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.15 (0.26), residues: 1103 helix: 0.72 (0.26), residues: 398 sheet: -0.40 (0.32), residues: 254 loop : -0.51 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 169 HIS 0.003 0.001 HIS A 322 PHE 0.023 0.002 PHE A 192 TYR 0.013 0.001 TYR A 354 ARG 0.003 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7961 (mm-30) REVERT: B 78 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7885 (mmmt) REVERT: B 145 TYR cc_start: 0.7460 (p90) cc_final: 0.7164 (p90) REVERT: B 259 GLN cc_start: 0.7021 (tp40) cc_final: 0.6751 (mm110) REVERT: B 264 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.7139 (m-10) REVERT: B 325 MET cc_start: 0.7790 (mmm) cc_final: 0.7568 (mmm) REVERT: C 32 LEU cc_start: 0.7539 (mt) cc_final: 0.7199 (tp) REVERT: C 35 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7679 (mm) REVERT: C 395 ILE cc_start: 0.7300 (pt) cc_final: 0.6957 (pt) REVERT: C 416 TRP cc_start: 0.7770 (m100) cc_final: 0.7033 (m100) REVERT: D 77 ARG cc_start: 0.7004 (mmm-85) cc_final: 0.6744 (mmm-85) REVERT: H 216 ILE cc_start: 0.8336 (mp) cc_final: 0.8067 (mt) outliers start: 15 outliers final: 4 residues processed: 180 average time/residue: 0.1910 time to fit residues: 47.2680 Evaluate side-chains 157 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 0.0170 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN H 39 GLN H 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.127616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.110290 restraints weight = 17564.946| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.31 r_work: 0.3692 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8325 Z= 0.224 Angle : 0.601 10.297 11353 Z= 0.309 Chirality : 0.043 0.149 1329 Planarity : 0.004 0.047 1450 Dihedral : 4.899 58.904 1191 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.66 % Allowed : 14.72 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.05 (0.26), residues: 1103 helix: 0.97 (0.27), residues: 400 sheet: -0.47 (0.32), residues: 255 loop : -0.57 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.019 0.002 PHE H 68 TYR 0.016 0.002 TYR H 190 ARG 0.003 0.000 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7040 (OUTLIER) cc_final: 0.6333 (p90) REVERT: A 349 ARG cc_start: 0.8230 (tpp80) cc_final: 0.7642 (mtt-85) REVERT: B 179 THR cc_start: 0.8014 (m) cc_final: 0.7797 (t) REVERT: B 259 GLN cc_start: 0.7261 (tp40) cc_final: 0.6967 (mm110) REVERT: C 35 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7669 (mm) REVERT: C 416 TRP cc_start: 0.7973 (m100) cc_final: 0.7172 (m100) REVERT: D 77 ARG cc_start: 0.7190 (mmm-85) cc_final: 0.6812 (mmm-85) REVERT: H 6 GLU cc_start: 0.5858 (mp0) cc_final: 0.5513 (mt-10) REVERT: H 216 ILE cc_start: 0.8335 (mp) cc_final: 0.7979 (mt) outliers start: 21 outliers final: 12 residues processed: 175 average time/residue: 0.2087 time to fit residues: 49.5374 Evaluate side-chains 163 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 14 optimal weight: 0.0030 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 32 GLN B 176 GLN H 232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.127527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.110085 restraints weight = 17318.297| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.33 r_work: 0.3686 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8325 Z= 0.226 Angle : 0.593 9.575 11353 Z= 0.302 Chirality : 0.043 0.146 1329 Planarity : 0.004 0.041 1450 Dihedral : 4.830 64.801 1191 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.17 % Allowed : 16.62 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.02 (0.26), residues: 1103 helix: 1.03 (0.27), residues: 400 sheet: -0.44 (0.32), residues: 253 loop : -0.60 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.017 0.002 PHE H 68 TYR 0.016 0.001 TYR H 190 ARG 0.003 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7136 (OUTLIER) cc_final: 0.6301 (p90) REVERT: A 282 SER cc_start: 0.7098 (m) cc_final: 0.6829 (p) REVERT: A 349 ARG cc_start: 0.8252 (tpp80) cc_final: 0.7732 (mtt-85) REVERT: B 176 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7662 (tp40) REVERT: B 179 THR cc_start: 0.8063 (m) cc_final: 0.7837 (t) REVERT: B 198 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8065 (pp) REVERT: B 259 GLN cc_start: 0.7197 (tp40) cc_final: 0.6895 (mm110) REVERT: C 35 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7674 (mm) REVERT: C 90 TYR cc_start: 0.6121 (m-80) cc_final: 0.5728 (m-80) REVERT: C 416 TRP cc_start: 0.8106 (m100) cc_final: 0.7430 (m100) REVERT: C 421 ILE cc_start: 0.7915 (mm) cc_final: 0.7570 (mt) REVERT: D 77 ARG cc_start: 0.6937 (mmm-85) cc_final: 0.6665 (mmm-85) REVERT: H 6 GLU cc_start: 0.5931 (mp0) cc_final: 0.5593 (mt-10) REVERT: H 216 ILE cc_start: 0.8278 (mp) cc_final: 0.8071 (mt) outliers start: 25 outliers final: 18 residues processed: 172 average time/residue: 0.2313 time to fit residues: 54.1755 Evaluate side-chains 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.126803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.109368 restraints weight = 17292.938| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.33 r_work: 0.3675 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8325 Z= 0.245 Angle : 0.596 9.226 11353 Z= 0.306 Chirality : 0.043 0.155 1329 Planarity : 0.004 0.038 1450 Dihedral : 4.834 67.771 1191 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.17 % Allowed : 17.64 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.08 (0.26), residues: 1103 helix: 1.02 (0.27), residues: 403 sheet: -0.52 (0.32), residues: 253 loop : -0.65 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.006 0.001 HIS B 225 PHE 0.019 0.002 PHE A 336 TYR 0.016 0.002 TYR H 190 ARG 0.005 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6202 (p90) REVERT: A 349 ARG cc_start: 0.8276 (tpp80) cc_final: 0.7781 (mtt-85) REVERT: B 198 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8052 (pp) REVERT: B 259 GLN cc_start: 0.7240 (tp40) cc_final: 0.6924 (mm110) REVERT: C 35 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7611 (mm) REVERT: C 90 TYR cc_start: 0.6060 (m-80) cc_final: 0.5667 (m-80) REVERT: C 374 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7913 (mtmm) REVERT: C 416 TRP cc_start: 0.8131 (m100) cc_final: 0.7514 (m100) REVERT: C 421 ILE cc_start: 0.8016 (mm) cc_final: 0.7681 (mt) REVERT: D 77 ARG cc_start: 0.7065 (mmm-85) cc_final: 0.6814 (mmm-85) REVERT: H 6 GLU cc_start: 0.5867 (mp0) cc_final: 0.5504 (mt-10) REVERT: H 216 ILE cc_start: 0.8259 (mp) cc_final: 0.8054 (mt) outliers start: 25 outliers final: 18 residues processed: 174 average time/residue: 0.2596 time to fit residues: 61.1703 Evaluate side-chains 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 46 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.127103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.109655 restraints weight = 17345.909| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.32 r_work: 0.3682 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8325 Z= 0.232 Angle : 0.586 9.356 11353 Z= 0.301 Chirality : 0.043 0.162 1329 Planarity : 0.004 0.037 1450 Dihedral : 4.794 69.431 1191 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.43 % Allowed : 17.77 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.08 (0.26), residues: 1103 helix: 1.04 (0.27), residues: 402 sheet: -0.57 (0.32), residues: 253 loop : -0.63 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS B 225 PHE 0.018 0.002 PHE H 68 TYR 0.015 0.002 TYR H 190 ARG 0.003 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6130 (p90) REVERT: A 349 ARG cc_start: 0.8356 (tpp80) cc_final: 0.7926 (mtt-85) REVERT: B 198 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8063 (pp) REVERT: B 259 GLN cc_start: 0.7214 (tp40) cc_final: 0.6921 (mm110) REVERT: C 35 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7571 (mm) REVERT: C 90 TYR cc_start: 0.6039 (m-80) cc_final: 0.5639 (m-80) REVERT: C 416 TRP cc_start: 0.8039 (m100) cc_final: 0.7521 (m100) REVERT: C 421 ILE cc_start: 0.7968 (mm) cc_final: 0.7696 (mt) REVERT: D 77 ARG cc_start: 0.6951 (mmm-85) cc_final: 0.6750 (mmm-85) REVERT: H 6 GLU cc_start: 0.5808 (mp0) cc_final: 0.5442 (mt-10) REVERT: H 208 SER cc_start: 0.8541 (t) cc_final: 0.8159 (m) outliers start: 27 outliers final: 18 residues processed: 177 average time/residue: 0.2166 time to fit residues: 52.7534 Evaluate side-chains 173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.127132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.109547 restraints weight = 17505.525| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.34 r_work: 0.3681 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8325 Z= 0.235 Angle : 0.584 9.226 11353 Z= 0.301 Chirality : 0.043 0.168 1329 Planarity : 0.004 0.037 1450 Dihedral : 4.769 69.856 1191 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.81 % Allowed : 18.53 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.09 (0.26), residues: 1103 helix: 1.07 (0.27), residues: 402 sheet: -0.61 (0.32), residues: 253 loop : -0.66 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 88 HIS 0.004 0.001 HIS B 225 PHE 0.023 0.002 PHE A 336 TYR 0.015 0.002 TYR H 190 ARG 0.002 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6152 (p90) REVERT: A 349 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7928 (mtt-85) REVERT: B 198 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8079 (pp) REVERT: B 259 GLN cc_start: 0.7226 (tp40) cc_final: 0.6932 (mm110) REVERT: C 35 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7539 (mm) REVERT: C 90 TYR cc_start: 0.6018 (m-80) cc_final: 0.5681 (m-80) REVERT: C 374 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7969 (mtmm) REVERT: C 416 TRP cc_start: 0.8072 (m100) cc_final: 0.7561 (m100) REVERT: C 421 ILE cc_start: 0.7966 (mm) cc_final: 0.7695 (mt) REVERT: H 208 SER cc_start: 0.8514 (t) cc_final: 0.8123 (m) outliers start: 30 outliers final: 20 residues processed: 171 average time/residue: 0.1886 time to fit residues: 44.4775 Evaluate side-chains 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 0.6980 chunk 97 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.127909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.110342 restraints weight = 17501.150| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.36 r_work: 0.3692 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8325 Z= 0.201 Angle : 0.571 8.941 11353 Z= 0.294 Chirality : 0.042 0.174 1329 Planarity : 0.004 0.038 1450 Dihedral : 4.697 73.002 1191 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.17 % Allowed : 19.80 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.03 (0.26), residues: 1103 helix: 1.18 (0.27), residues: 397 sheet: -0.59 (0.31), residues: 261 loop : -0.52 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 88 HIS 0.006 0.001 HIS A 322 PHE 0.019 0.001 PHE A 190 TYR 0.014 0.001 TYR H 190 ARG 0.004 0.000 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.5926 (p90) REVERT: A 349 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7746 (mtt-85) REVERT: B 127 LYS cc_start: 0.7995 (ptpt) cc_final: 0.7674 (ptpt) REVERT: B 198 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8011 (pp) REVERT: B 259 GLN cc_start: 0.6910 (tp40) cc_final: 0.6649 (mm110) REVERT: C 35 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7555 (mm) REVERT: C 90 TYR cc_start: 0.5934 (m-80) cc_final: 0.5733 (m-80) REVERT: C 374 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7857 (mtmm) REVERT: C 396 PHE cc_start: 0.5752 (m-80) cc_final: 0.5504 (m-80) REVERT: C 416 TRP cc_start: 0.7922 (m100) cc_final: 0.7364 (m100) REVERT: C 421 ILE cc_start: 0.7882 (mm) cc_final: 0.7609 (mt) REVERT: D 77 ARG cc_start: 0.6639 (mmm-85) cc_final: 0.6341 (mmm-85) REVERT: H 208 SER cc_start: 0.8365 (t) cc_final: 0.7939 (m) outliers start: 25 outliers final: 20 residues processed: 171 average time/residue: 0.2222 time to fit residues: 51.8480 Evaluate side-chains 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 75 optimal weight: 0.0030 chunk 96 optimal weight: 0.0070 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 chunk 61 optimal weight: 0.2980 overall best weight: 0.1906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 32 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.130270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.112707 restraints weight = 17565.136| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.39 r_work: 0.3736 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8325 Z= 0.158 Angle : 0.565 8.634 11353 Z= 0.290 Chirality : 0.041 0.180 1329 Planarity : 0.004 0.038 1450 Dihedral : 4.556 79.929 1191 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.16 % Allowed : 20.81 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.15 (0.27), residues: 1103 helix: 1.31 (0.27), residues: 397 sheet: -0.44 (0.31), residues: 277 loop : -0.55 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 88 HIS 0.003 0.001 HIS B 225 PHE 0.019 0.001 PHE A 190 TYR 0.012 0.001 TYR A 354 ARG 0.004 0.000 ARG C 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7658 (mtt-85) REVERT: B 145 TYR cc_start: 0.7407 (p90) cc_final: 0.7029 (p90) REVERT: B 198 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8046 (pp) REVERT: C 35 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7586 (mm) REVERT: C 416 TRP cc_start: 0.7885 (m100) cc_final: 0.7437 (m100) REVERT: C 420 CYS cc_start: 0.7725 (m) cc_final: 0.7504 (m) REVERT: C 421 ILE cc_start: 0.7925 (mm) cc_final: 0.7622 (mt) REVERT: H 73 ASP cc_start: 0.6468 (t70) cc_final: 0.6202 (t70) REVERT: H 208 SER cc_start: 0.8344 (t) cc_final: 0.7935 (m) outliers start: 17 outliers final: 11 residues processed: 171 average time/residue: 0.2028 time to fit residues: 46.9250 Evaluate side-chains 164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0000 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 32 GLN H 39 GLN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.128513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.111193 restraints weight = 17134.520| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.32 r_work: 0.3713 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8325 Z= 0.193 Angle : 0.585 8.469 11353 Z= 0.300 Chirality : 0.042 0.179 1329 Planarity : 0.004 0.037 1450 Dihedral : 4.679 85.833 1191 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.03 % Allowed : 21.95 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1103 helix: 1.27 (0.27), residues: 397 sheet: -0.49 (0.30), residues: 279 loop : -0.52 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 88 HIS 0.006 0.001 HIS B 225 PHE 0.020 0.002 PHE A 190 TYR 0.014 0.001 TYR H 190 ARG 0.004 0.000 ARG H 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8276 (tpp80) cc_final: 0.7824 (mtt-85) REVERT: B 127 LYS cc_start: 0.7891 (ptpt) cc_final: 0.7510 (ptpt) REVERT: B 145 TYR cc_start: 0.7587 (p90) cc_final: 0.7369 (p90) REVERT: B 198 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8105 (pp) REVERT: C 35 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7647 (mm) REVERT: C 416 TRP cc_start: 0.8078 (m100) cc_final: 0.7598 (m100) REVERT: C 420 CYS cc_start: 0.7981 (m) cc_final: 0.7763 (m) REVERT: C 421 ILE cc_start: 0.8020 (mm) cc_final: 0.7738 (mt) REVERT: H 73 ASP cc_start: 0.6536 (t70) cc_final: 0.6222 (t70) REVERT: H 208 SER cc_start: 0.8381 (t) cc_final: 0.7991 (m) outliers start: 16 outliers final: 12 residues processed: 162 average time/residue: 0.1935 time to fit residues: 43.2403 Evaluate side-chains 165 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.127455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.109920 restraints weight = 17464.200| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.30 r_work: 0.3689 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8325 Z= 0.249 Angle : 0.613 11.536 11353 Z= 0.313 Chirality : 0.043 0.186 1329 Planarity : 0.004 0.038 1450 Dihedral : 4.855 85.942 1191 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.28 % Allowed : 21.32 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.08 (0.26), residues: 1103 helix: 1.09 (0.27), residues: 403 sheet: -0.68 (0.31), residues: 269 loop : -0.60 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 88 HIS 0.005 0.001 HIS B 225 PHE 0.028 0.002 PHE A 336 TYR 0.015 0.002 TYR H 190 ARG 0.005 0.000 ARG H 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5229.43 seconds wall clock time: 92 minutes 51.00 seconds (5571.00 seconds total)