Starting phenix.real_space_refine on Sun May 11 22:17:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9a_35263/05_2025/8i9a_35263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9a_35263/05_2025/8i9a_35263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i9a_35263/05_2025/8i9a_35263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9a_35263/05_2025/8i9a_35263.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9a_35263/05_2025/8i9a_35263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9a_35263/05_2025/8i9a_35263.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 51 5.16 5 C 5353 2.51 5 N 1458 2.21 5 O 1547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8409 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1858 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 3 Chain: "B" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2415 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 400 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2006 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 7.42, per 1000 atoms: 0.88 Number of scatterers: 8409 At special positions: 0 Unit cell: (84.64, 119.6, 122.36, 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 51 16.00 O 1547 8.00 N 1458 7.00 C 5353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " 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 Links applied TRANS " DAL D 9 " - " LEU D 8 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 9 " Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 39.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.539A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.516A pdb=" N ASN A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 4.141A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.595A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.134A 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 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.792A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.534A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix 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 helix chain 'C' and resid 20 through 50 Proline residue: C 39 - end of helix removed outlier: 3.545A pdb=" N VAL C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 74 removed outlier: 3.519A pdb=" N TRP C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 85 removed outlier: 4.201A pdb=" N SER C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 126 Proline residue: C 99 - end of helix removed outlier: 3.687A pdb=" N ASN C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.528A 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 161 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 332 through 345 Processing helix chain 'C' and resid 345 through 363 removed outlier: 3.550A pdb=" N VAL C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 403 Proline residue: C 392 - end of helix removed outlier: 3.659A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 435 removed outlier: 3.924A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 439 through 450 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.822A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.755A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.531A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.008A 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: 6.949A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.674A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.679A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.624A 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: 3.737A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.976A 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 278 removed outlier: 3.924A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.005A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.670A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.877A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.131A pdb=" N VAL H 147 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 162 through 163 460 hydrogen bonds defined for protein. 1284 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: 2.67 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1559 1.33 - 1.45: 2235 1.45 - 1.57: 4728 1.57 - 1.69: 0 1.69 - 1.82: 68 Bond restraints: 8590 Sorted by residual: bond pdb=" C PRO G 60 " pdb=" O PRO G 60 " ideal model delta sigma weight residual 1.239 1.204 0.035 1.22e-02 6.72e+03 8.11e+00 bond pdb=" N ARG A 231 " pdb=" CA ARG A 231 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.30e-02 5.92e+03 7.11e+00 bond pdb=" N VAL C 388 " pdb=" CA VAL C 388 " ideal model delta sigma weight residual 1.461 1.491 -0.029 1.17e-02 7.31e+03 6.31e+00 bond pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.25e-02 6.40e+03 5.81e+00 bond pdb=" CA PHE A 208 " pdb=" CB PHE A 208 " ideal model delta sigma weight residual 1.526 1.565 -0.039 1.68e-02 3.54e+03 5.34e+00 ... (remaining 8585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 11132 1.60 - 3.20: 471 3.20 - 4.80: 77 4.80 - 6.40: 13 6.40 - 8.00: 1 Bond angle restraints: 11694 Sorted by residual: angle pdb=" C PHE A 273 " pdb=" N LYS A 274 " pdb=" CA LYS A 274 " ideal model delta sigma weight residual 120.44 115.14 5.30 1.30e+00 5.92e-01 1.66e+01 angle pdb=" N ASP A 272 " pdb=" CA ASP A 272 " pdb=" C ASP A 272 " ideal model delta sigma weight residual 111.07 107.05 4.02 1.07e+00 8.73e-01 1.41e+01 angle pdb=" N LYS A 274 " pdb=" CA LYS A 274 " pdb=" C LYS A 274 " ideal model delta sigma weight residual 111.07 107.10 3.97 1.07e+00 8.73e-01 1.37e+01 angle pdb=" N GLU A 21 " pdb=" CA GLU A 21 " pdb=" C GLU A 21 " ideal model delta sigma weight residual 111.07 107.25 3.82 1.07e+00 8.73e-01 1.27e+01 angle pdb=" N PRO C 156 " pdb=" CA PRO C 156 " pdb=" C PRO C 156 " ideal model delta sigma weight residual 113.78 108.15 5.63 1.62e+00 3.81e-01 1.21e+01 ... (remaining 11689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4599 17.97 - 35.94: 353 35.94 - 53.90: 62 53.90 - 71.87: 20 71.87 - 89.84: 6 Dihedral angle restraints: 5040 sinusoidal: 1775 harmonic: 3265 Sorted by residual: dihedral pdb=" CA ASN A 279 " pdb=" C ASN A 279 " pdb=" N ARG A 280 " pdb=" CA ARG A 280 " ideal model delta harmonic sigma weight residual 180.00 -152.35 -27.65 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA PRO G 53 " pdb=" C PRO G 53 " pdb=" N VAL G 54 " pdb=" CA VAL G 54 " ideal model delta harmonic sigma weight residual 180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1188 0.071 - 0.142: 155 0.142 - 0.213: 6 0.213 - 0.284: 0 0.284 - 0.355: 1 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA ASN B 313 " pdb=" N ASN B 313 " pdb=" C ASN B 313 " pdb=" CB ASN B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB VAL C 388 " pdb=" CA VAL C 388 " pdb=" CG1 VAL C 388 " pdb=" CG2 VAL C 388 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ARG A 333 " pdb=" N ARG A 333 " pdb=" C ARG A 333 " pdb=" CB ARG A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 1347 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 325 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 326 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 340 " 0.010 2.00e-02 2.50e+03 1.21e-02 2.56e+00 pdb=" CG PHE A 340 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 340 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 340 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 340 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 340 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 347 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO C 348 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 348 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 348 " -0.022 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 41 2.55 - 3.14: 7128 3.14 - 3.72: 13063 3.72 - 4.31: 18059 4.31 - 4.90: 30403 Nonbonded interactions: 68694 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 1.959 3.040 nonbonded pdb=" N GLU G 47 " pdb=" OE1 GLU G 47 " model vdw 2.100 3.120 nonbonded pdb=" O MET C 138 " pdb=" OG SER C 141 " model vdw 2.246 3.040 nonbonded pdb=" NH1 ARG C 340 " pdb=" OXT ARG D 10 " model vdw 2.290 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.302 3.040 ... (remaining 68689 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: 0.010 Normalize map: mean=0, sd=1: 4.530 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.450 Find NCS groups from input model: 0.100 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 0.041 8594 Z= 0.205 Angle : 0.759 8.005 11703 Z= 0.443 Chirality : 0.046 0.355 1350 Planarity : 0.005 0.052 1494 Dihedral : 14.157 89.840 2916 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.19 % Allowed : 12.53 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.11 (0.26), residues: 1103 helix: 0.57 (0.25), residues: 390 sheet: -0.38 (0.30), residues: 293 loop : -0.24 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.006 0.002 HIS H 167 PHE 0.028 0.002 PHE A 340 TYR 0.016 0.002 TYR C 393 ARG 0.007 0.001 ARG B 68 Details of bonding type rmsd link_TRANS : bond 0.00209 ( 1) link_TRANS : angle 0.91325 ( 3) hydrogen bonds : bond 0.14764 ( 455) hydrogen bonds : angle 7.33684 ( 1284) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.76610 ( 6) covalent geometry : bond 0.00399 ( 8590) covalent geometry : angle 0.75845 (11694) *********************** 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 215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6924 (mmm) cc_final: 0.6705 (mpp) REVERT: A 274 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9039 (mttp) REVERT: A 391 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5514 (m-80) REVERT: B 67 SER cc_start: 0.8448 (t) cc_final: 0.7879 (t) REVERT: H 184 SER cc_start: 0.9289 (p) cc_final: 0.8987 (m) REVERT: D 6 MET cc_start: 0.8072 (tpp) cc_final: 0.7682 (tpp) outliers start: 10 outliers final: 2 residues processed: 212 average time/residue: 0.2285 time to fit residues: 63.4467 Evaluate side-chains 177 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 434 LEU 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: 0.8980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.187393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142172 restraints weight = 10851.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142237 restraints weight = 6668.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144616 restraints weight = 5005.594| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8594 Z= 0.180 Angle : 0.663 7.858 11703 Z= 0.353 Chirality : 0.045 0.185 1350 Planarity : 0.005 0.054 1494 Dihedral : 6.025 54.607 1216 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.03 % Allowed : 13.48 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.50 (0.26), residues: 1103 helix: 1.41 (0.26), residues: 395 sheet: -0.33 (0.30), residues: 290 loop : -0.05 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 297 HIS 0.006 0.001 HIS C 394 PHE 0.022 0.002 PHE A 208 TYR 0.014 0.002 TYR A 318 ARG 0.005 0.001 ARG D 10 Details of bonding type rmsd link_TRANS : bond 0.00204 ( 1) link_TRANS : angle 1.12210 ( 3) hydrogen bonds : bond 0.04730 ( 455) hydrogen bonds : angle 5.67257 ( 1284) SS BOND : bond 0.00235 ( 3) SS BOND : angle 1.15955 ( 6) covalent geometry : bond 0.00409 ( 8590) covalent geometry : angle 0.66247 (11694) *********************** 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 212 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.8084 (p90) cc_final: 0.7859 (p90) REVERT: A 309 GLU cc_start: 0.8726 (pm20) cc_final: 0.8390 (pm20) REVERT: A 330 GLU cc_start: 0.8004 (tp30) cc_final: 0.7554 (tp30) REVERT: B 234 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: H 184 SER cc_start: 0.9340 (p) cc_final: 0.9023 (m) REVERT: C 92 ARG cc_start: 0.7083 (tpt-90) cc_final: 0.5955 (tmm-80) REVERT: C 160 TYR cc_start: 0.6791 (t80) cc_final: 0.6454 (t80) REVERT: C 414 MET cc_start: 0.7858 (ppp) cc_final: 0.7622 (ppp) REVERT: C 418 HIS cc_start: 0.7649 (m90) cc_final: 0.7424 (m90) REVERT: C 434 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8438 (tt) outliers start: 17 outliers final: 10 residues processed: 204 average time/residue: 0.2238 time to fit residues: 61.3475 Evaluate side-chains 190 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 434 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 6.9990 chunk 70 optimal weight: 0.0050 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN H 167 HIS H 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.188610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144230 restraints weight = 10937.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144587 restraints weight = 7260.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146482 restraints weight = 5599.710| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8594 Z= 0.156 Angle : 0.615 7.124 11703 Z= 0.324 Chirality : 0.044 0.188 1350 Planarity : 0.004 0.057 1494 Dihedral : 5.481 58.344 1212 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.39 % Allowed : 15.75 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.60 (0.26), residues: 1103 helix: 1.56 (0.26), residues: 407 sheet: -0.35 (0.30), residues: 277 loop : -0.07 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 88 HIS 0.007 0.001 HIS C 394 PHE 0.026 0.002 PHE C 34 TYR 0.015 0.002 TYR A 318 ARG 0.005 0.001 ARG H 18 Details of bonding type rmsd link_TRANS : bond 0.00229 ( 1) link_TRANS : angle 1.05999 ( 3) hydrogen bonds : bond 0.03930 ( 455) hydrogen bonds : angle 5.36228 ( 1284) SS BOND : bond 0.00337 ( 3) SS BOND : angle 0.90920 ( 6) covalent geometry : bond 0.00351 ( 8590) covalent geometry : angle 0.61466 (11694) *********************** 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 219 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 208 PHE cc_start: 0.8233 (t80) cc_final: 0.8028 (t80) REVERT: A 280 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7793 (ttp-170) REVERT: A 309 GLU cc_start: 0.8763 (pm20) cc_final: 0.8485 (pm20) REVERT: B 168 LEU cc_start: 0.8827 (tp) cc_final: 0.8388 (tt) REVERT: B 234 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: H 140 MET cc_start: 0.8015 (mmm) cc_final: 0.7725 (mmm) REVERT: H 184 SER cc_start: 0.9454 (p) cc_final: 0.9121 (m) REVERT: C 34 PHE cc_start: 0.8731 (t80) cc_final: 0.8514 (t80) REVERT: C 92 ARG cc_start: 0.7056 (tpt-90) cc_final: 0.5881 (tmm-80) REVERT: C 160 TYR cc_start: 0.6806 (t80) cc_final: 0.6337 (t80) REVERT: C 355 CYS cc_start: 0.8486 (m) cc_final: 0.8059 (m) REVERT: C 418 HIS cc_start: 0.7599 (m90) cc_final: 0.7362 (m90) outliers start: 20 outliers final: 15 residues processed: 206 average time/residue: 0.2245 time to fit residues: 61.3116 Evaluate side-chains 190 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 174 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN H 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.188713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144198 restraints weight = 10962.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143664 restraints weight = 6946.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.146466 restraints weight = 5128.178| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8594 Z= 0.148 Angle : 0.598 9.753 11703 Z= 0.312 Chirality : 0.043 0.156 1350 Planarity : 0.004 0.056 1494 Dihedral : 5.032 59.388 1210 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.70 % Allowed : 15.87 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.74 (0.26), residues: 1103 helix: 1.77 (0.26), residues: 405 sheet: -0.46 (0.30), residues: 277 loop : 0.06 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 88 HIS 0.007 0.001 HIS C 394 PHE 0.025 0.002 PHE A 340 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG C 134 Details of bonding type rmsd link_TRANS : bond 0.00194 ( 1) link_TRANS : angle 1.01788 ( 3) hydrogen bonds : bond 0.03673 ( 455) hydrogen bonds : angle 5.14283 ( 1284) SS BOND : bond 0.00164 ( 3) SS BOND : angle 0.90956 ( 6) covalent geometry : bond 0.00330 ( 8590) covalent geometry : angle 0.59716 (11694) *********************** 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 230 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 208 PHE cc_start: 0.8226 (t80) cc_final: 0.8022 (t80) REVERT: A 280 ARG cc_start: 0.8170 (ptm160) cc_final: 0.7762 (ttp-170) REVERT: A 309 GLU cc_start: 0.8855 (pm20) cc_final: 0.8550 (pm20) REVERT: A 330 GLU cc_start: 0.7800 (tp30) cc_final: 0.7476 (tp30) REVERT: B 168 LEU cc_start: 0.8814 (tp) cc_final: 0.8376 (tt) REVERT: B 198 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7574 (pp) REVERT: B 215 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6647 (tt0) REVERT: B 234 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: B 292 PHE cc_start: 0.8741 (m-10) cc_final: 0.8255 (m-10) REVERT: G 27 ARG cc_start: 0.8451 (ttm110) cc_final: 0.7693 (ttm110) REVERT: H 140 MET cc_start: 0.8090 (mmm) cc_final: 0.7878 (mmm) REVERT: H 184 SER cc_start: 0.9456 (p) cc_final: 0.9074 (m) REVERT: C 92 ARG cc_start: 0.6814 (tpt-90) cc_final: 0.5675 (tmm-80) REVERT: C 107 PHE cc_start: 0.6174 (m-80) cc_final: 0.5942 (m-80) REVERT: C 355 CYS cc_start: 0.8511 (m) cc_final: 0.8075 (m) REVERT: C 418 HIS cc_start: 0.7546 (m90) cc_final: 0.7328 (m90) REVERT: D 6 MET cc_start: 0.8318 (tpp) cc_final: 0.7964 (tpp) outliers start: 31 outliers final: 16 residues processed: 217 average time/residue: 0.2025 time to fit residues: 59.9740 Evaluate side-chains 201 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 172 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 58 optimal weight: 0.0000 chunk 99 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.190213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146540 restraints weight = 10767.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147133 restraints weight = 6059.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149422 restraints weight = 4671.821| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8594 Z= 0.132 Angle : 0.610 10.418 11703 Z= 0.312 Chirality : 0.043 0.283 1350 Planarity : 0.004 0.057 1494 Dihedral : 4.726 59.700 1208 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.10 % Allowed : 17.42 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.83 (0.26), residues: 1103 helix: 1.80 (0.26), residues: 405 sheet: -0.33 (0.30), residues: 275 loop : 0.08 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 88 HIS 0.010 0.001 HIS C 394 PHE 0.018 0.002 PHE H 239 TYR 0.012 0.001 TYR H 190 ARG 0.003 0.000 ARG C 134 Details of bonding type rmsd link_TRANS : bond 0.00266 ( 1) link_TRANS : angle 1.10626 ( 3) hydrogen bonds : bond 0.03520 ( 455) hydrogen bonds : angle 5.08909 ( 1284) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.69645 ( 6) covalent geometry : bond 0.00291 ( 8590) covalent geometry : angle 0.60964 (11694) *********************** 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 211 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8785 (pm20) cc_final: 0.8514 (pm20) REVERT: B 168 LEU cc_start: 0.8824 (tp) cc_final: 0.8393 (tt) REVERT: B 198 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7603 (pp) REVERT: B 215 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6759 (tt0) REVERT: B 234 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: B 292 PHE cc_start: 0.8716 (m-10) cc_final: 0.8221 (m-10) REVERT: H 140 MET cc_start: 0.8064 (mmm) cc_final: 0.7763 (mmm) REVERT: H 184 SER cc_start: 0.9433 (p) cc_final: 0.9018 (m) REVERT: C 355 CYS cc_start: 0.8493 (m) cc_final: 0.8092 (m) REVERT: C 418 HIS cc_start: 0.7498 (m90) cc_final: 0.7253 (m90) outliers start: 26 outliers final: 16 residues processed: 200 average time/residue: 0.1986 time to fit residues: 54.3106 Evaluate side-chains 192 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.186193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143118 restraints weight = 11211.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142281 restraints weight = 7195.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145072 restraints weight = 5381.798| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8594 Z= 0.190 Angle : 0.641 9.220 11703 Z= 0.331 Chirality : 0.045 0.284 1350 Planarity : 0.004 0.058 1494 Dihedral : 4.821 59.626 1208 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.06 % Allowed : 18.74 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.69 (0.26), residues: 1103 helix: 1.78 (0.26), residues: 401 sheet: -0.46 (0.30), residues: 276 loop : -0.03 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 88 HIS 0.007 0.001 HIS C 394 PHE 0.024 0.002 PHE A 208 TYR 0.016 0.002 TYR A 318 ARG 0.004 0.000 ARG C 161 Details of bonding type rmsd link_TRANS : bond 0.00150 ( 1) link_TRANS : angle 0.90614 ( 3) hydrogen bonds : bond 0.03739 ( 455) hydrogen bonds : angle 5.16385 ( 1284) SS BOND : bond 0.00272 ( 3) SS BOND : angle 0.77075 ( 6) covalent geometry : bond 0.00436 ( 8590) covalent geometry : angle 0.64043 (11694) *********************** 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 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8771 (pm20) cc_final: 0.8500 (pm20) REVERT: B 168 LEU cc_start: 0.8840 (tp) cc_final: 0.8369 (tt) REVERT: B 198 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7679 (pp) REVERT: B 215 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6921 (tt0) REVERT: B 234 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: H 37 VAL cc_start: 0.7973 (t) cc_final: 0.6865 (p) REVERT: H 184 SER cc_start: 0.9445 (p) cc_final: 0.9010 (m) REVERT: C 418 HIS cc_start: 0.7510 (m90) cc_final: 0.7280 (m90) outliers start: 34 outliers final: 22 residues processed: 205 average time/residue: 0.2140 time to fit residues: 59.8974 Evaluate side-chains 204 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 225 HIS H 183 GLN ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.189569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147328 restraints weight = 11273.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147050 restraints weight = 6883.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149681 restraints weight = 5285.551| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8594 Z= 0.154 Angle : 0.641 10.787 11703 Z= 0.328 Chirality : 0.044 0.277 1350 Planarity : 0.004 0.059 1494 Dihedral : 4.753 58.583 1208 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.34 % Allowed : 19.57 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.70 (0.26), residues: 1103 helix: 1.75 (0.26), residues: 402 sheet: -0.47 (0.30), residues: 276 loop : 0.02 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 88 HIS 0.005 0.001 HIS C 394 PHE 0.019 0.002 PHE C 151 TYR 0.014 0.001 TYR A 318 ARG 0.007 0.000 ARG C 161 Details of bonding type rmsd link_TRANS : bond 0.00189 ( 1) link_TRANS : angle 0.90009 ( 3) hydrogen bonds : bond 0.03597 ( 455) hydrogen bonds : angle 5.13802 ( 1284) SS BOND : bond 0.00274 ( 3) SS BOND : angle 0.80783 ( 6) covalent geometry : bond 0.00347 ( 8590) covalent geometry : angle 0.64062 (11694) *********************** 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 215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 230 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6543 (mt-10) REVERT: A 309 GLU cc_start: 0.8720 (pm20) cc_final: 0.8475 (pm20) REVERT: A 330 GLU cc_start: 0.7814 (tp30) cc_final: 0.7510 (tp30) REVERT: B 168 LEU cc_start: 0.8824 (tp) cc_final: 0.8347 (tt) REVERT: B 198 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7590 (pp) REVERT: B 215 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6799 (tt0) REVERT: B 234 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: B 292 PHE cc_start: 0.8605 (m-10) cc_final: 0.8257 (m-10) REVERT: H 184 SER cc_start: 0.9433 (p) cc_final: 0.8994 (m) REVERT: C 418 HIS cc_start: 0.7479 (m90) cc_final: 0.7263 (m90) outliers start: 28 outliers final: 21 residues processed: 201 average time/residue: 0.2126 time to fit residues: 58.6022 Evaluate side-chains 195 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.0000 chunk 94 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS H 183 GLN ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.190691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146483 restraints weight = 10919.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147831 restraints weight = 6502.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149601 restraints weight = 4864.986| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8594 Z= 0.126 Angle : 0.630 11.401 11703 Z= 0.322 Chirality : 0.044 0.306 1350 Planarity : 0.004 0.059 1494 Dihedral : 4.592 57.861 1208 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.39 % Allowed : 20.17 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.74 (0.26), residues: 1103 helix: 1.76 (0.26), residues: 404 sheet: -0.41 (0.32), residues: 254 loop : -0.01 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 88 HIS 0.006 0.001 HIS C 394 PHE 0.026 0.002 PHE A 208 TYR 0.017 0.001 TYR C 160 ARG 0.003 0.000 ARG G 27 Details of bonding type rmsd link_TRANS : bond 0.00226 ( 1) link_TRANS : angle 0.94969 ( 3) hydrogen bonds : bond 0.03463 ( 455) hydrogen bonds : angle 4.91575 ( 1284) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.81656 ( 6) covalent geometry : bond 0.00275 ( 8590) covalent geometry : angle 0.62995 (11694) *********************** 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 207 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.894 Fit side-chains REVERT: A 218 ASN cc_start: 0.8428 (p0) cc_final: 0.8166 (p0) REVERT: A 309 GLU cc_start: 0.8752 (pm20) cc_final: 0.8520 (pm20) REVERT: B 63 TRP cc_start: 0.8330 (m100) cc_final: 0.8084 (m100) REVERT: B 168 LEU cc_start: 0.8842 (tp) cc_final: 0.8364 (tt) REVERT: B 198 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7609 (pp) REVERT: B 215 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6737 (tt0) REVERT: B 234 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: B 292 PHE cc_start: 0.8588 (m-10) cc_final: 0.8182 (m-10) REVERT: H 184 SER cc_start: 0.9461 (p) cc_final: 0.9000 (m) REVERT: C 340 ARG cc_start: 0.6666 (ptp-170) cc_final: 0.6051 (ptm160) REVERT: D 6 MET cc_start: 0.8330 (tpp) cc_final: 0.7694 (tpp) outliers start: 20 outliers final: 14 residues processed: 200 average time/residue: 0.2036 time to fit residues: 55.5724 Evaluate side-chains 190 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.188017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145954 restraints weight = 10907.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144661 restraints weight = 6852.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146075 restraints weight = 5652.760| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8594 Z= 0.175 Angle : 0.677 11.615 11703 Z= 0.347 Chirality : 0.044 0.304 1350 Planarity : 0.004 0.058 1494 Dihedral : 4.680 58.178 1208 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.63 % Allowed : 20.64 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.64 (0.26), residues: 1103 helix: 1.76 (0.26), residues: 399 sheet: -0.42 (0.32), residues: 264 loop : -0.16 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 88 HIS 0.004 0.001 HIS C 418 PHE 0.026 0.002 PHE A 208 TYR 0.013 0.002 TYR B 111 ARG 0.007 0.000 ARG B 52 Details of bonding type rmsd link_TRANS : bond 0.00155 ( 1) link_TRANS : angle 0.85089 ( 3) hydrogen bonds : bond 0.03709 ( 455) hydrogen bonds : angle 5.05623 ( 1284) SS BOND : bond 0.00180 ( 3) SS BOND : angle 0.86184 ( 6) covalent geometry : bond 0.00397 ( 8590) covalent geometry : angle 0.67657 (11694) *********************** 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 200 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8450 (p0) cc_final: 0.8183 (p0) REVERT: A 309 GLU cc_start: 0.8764 (pm20) cc_final: 0.8530 (pm20) REVERT: B 168 LEU cc_start: 0.8893 (tp) cc_final: 0.8417 (tt) REVERT: B 198 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7586 (pp) REVERT: B 215 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6786 (tt0) REVERT: B 234 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: B 292 PHE cc_start: 0.8619 (m-10) cc_final: 0.8171 (m-10) REVERT: H 18 ARG cc_start: 0.7542 (ttt180) cc_final: 0.7265 (ttt180) REVERT: H 37 VAL cc_start: 0.7713 (t) cc_final: 0.6591 (p) REVERT: H 184 SER cc_start: 0.9473 (p) cc_final: 0.8994 (m) REVERT: D 6 MET cc_start: 0.8383 (tpp) cc_final: 0.7718 (tpp) outliers start: 22 outliers final: 20 residues processed: 191 average time/residue: 0.2077 time to fit residues: 54.1045 Evaluate side-chains 193 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 53 optimal weight: 0.4980 chunk 44 optimal weight: 0.0030 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.190322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.147749 restraints weight = 10778.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147413 restraints weight = 6711.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.149555 restraints weight = 5416.320| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8594 Z= 0.135 Angle : 0.657 12.175 11703 Z= 0.335 Chirality : 0.043 0.289 1350 Planarity : 0.004 0.057 1494 Dihedral : 4.579 57.579 1208 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.27 % Allowed : 21.00 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.74 (0.26), residues: 1103 helix: 1.82 (0.26), residues: 402 sheet: -0.40 (0.32), residues: 265 loop : -0.06 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 88 HIS 0.004 0.001 HIS H 35 PHE 0.028 0.002 PHE A 340 TYR 0.020 0.001 TYR C 160 ARG 0.007 0.000 ARG B 52 Details of bonding type rmsd link_TRANS : bond 0.00207 ( 1) link_TRANS : angle 0.94269 ( 3) hydrogen bonds : bond 0.03550 ( 455) hydrogen bonds : angle 4.95756 ( 1284) SS BOND : bond 0.00151 ( 3) SS BOND : angle 0.80991 ( 6) covalent geometry : bond 0.00297 ( 8590) covalent geometry : angle 0.65657 (11694) ********************** 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 204 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8409 (p0) cc_final: 0.8157 (p0) REVERT: A 309 GLU cc_start: 0.8715 (pm20) cc_final: 0.8503 (pm20) REVERT: B 168 LEU cc_start: 0.8849 (tp) cc_final: 0.8365 (tt) REVERT: B 198 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7621 (pp) REVERT: B 215 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6815 (tt0) REVERT: B 234 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: B 292 PHE cc_start: 0.8549 (m-10) cc_final: 0.8126 (m-10) REVERT: H 18 ARG cc_start: 0.7512 (ttt180) cc_final: 0.7291 (ttt180) REVERT: H 184 SER cc_start: 0.9479 (p) cc_final: 0.9000 (m) REVERT: C 340 ARG cc_start: 0.6649 (ptp-170) cc_final: 0.6122 (ptm160) REVERT: D 6 MET cc_start: 0.8373 (tpp) cc_final: 0.7728 (tpp) outliers start: 19 outliers final: 16 residues processed: 196 average time/residue: 0.2023 time to fit residues: 54.6173 Evaluate side-chains 196 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 0.0770 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.0040 chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.190188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147364 restraints weight = 10881.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146348 restraints weight = 7121.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149081 restraints weight = 5624.815| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8594 Z= 0.138 Angle : 0.663 12.445 11703 Z= 0.336 Chirality : 0.044 0.297 1350 Planarity : 0.005 0.057 1494 Dihedral : 4.586 57.306 1208 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.51 % Allowed : 20.88 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.77 (0.26), residues: 1103 helix: 1.82 (0.26), residues: 399 sheet: -0.45 (0.32), residues: 254 loop : 0.04 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 88 HIS 0.011 0.001 HIS B 225 PHE 0.021 0.002 PHE C 151 TYR 0.014 0.001 TYR B 111 ARG 0.007 0.000 ARG B 52 Details of bonding type rmsd link_TRANS : bond 0.00201 ( 1) link_TRANS : angle 0.91758 ( 3) hydrogen bonds : bond 0.03529 ( 455) hydrogen bonds : angle 4.94793 ( 1284) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.78223 ( 6) covalent geometry : bond 0.00311 ( 8590) covalent geometry : angle 0.66238 (11694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.18 seconds wall clock time: 52 minutes 53.26 seconds (3173.26 seconds total)