Starting phenix.real_space_refine on Thu Jul 2 11:11:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i9a_35263/07_2026/8i9a_35263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9a_35263/07_2026/8i9a_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8i9a_35263/07_2026/8i9a_35263.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i9a_35263/07_2026/8i9a_35263.cif" model { file = "/net/cci-nas-00/data/ceres_data/8i9a_35263/07_2026/8i9a_35263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9a_35263/07_2026/8i9a_35263.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i9a_35263/07_2026/8i9a_35263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9a_35263/07_2026/8i9a_35263.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'GLU:plan': 6, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 2} 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, 'ASP:plan': 2, 'ARG:plan': 3} 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: {'TRP:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} 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} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.84, per 1000 atoms: 0.22 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: 0.64 Conformation dependent library (CDL) restraints added in 420.5 milliseconds 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: 0.27 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: 1.37 Time building geometry restraints manager: 0.89 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: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.760 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 6.81 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG B 68 TYR 0.016 0.002 TYR C 393 PHE 0.028 0.002 PHE A 340 TRP 0.017 0.002 TRP A 234 HIS 0.006 0.002 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.21 ( 8590) covalent geometry : angle 0.75845 / 0.44 (11694) SS BOND : bond 0.00179 / 0.09 ( 3) SS BOND : angle 0.76610 / 0.36 ( 6) hydrogen bonds : bond 0.14764 / 10.14 ( 455) hydrogen bonds : angle 7.33684 / 5.07 ( 1284) link_TRANS : bond 0.00209 / 0.11 ( 1) link_TRANS : angle 0.91325 / 0.46 ( 3) *********************** 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 : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6924 (mmm) cc_final: 0.6704 (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: 0.7880 (t) REVERT: H 184 SER cc_start: 0.9289 (p) cc_final: 0.8988 (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: 0.1109 time to fit residues: 31.2212 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 : 0.323 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.189198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146051 restraints weight = 10766.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145393 restraints weight = 6290.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147738 restraints weight = 5108.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150540 restraints weight = 3725.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150578 restraints weight = 2984.390| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1577 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= 0.153 Angle : 0.639 7.649 11703 Z= 0.339 Chirality : 0.045 0.174 1350 Planarity : 0.004 0.052 1494 Dihedral : 5.886 55.220 1216 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.67 % Allowed : 13.37 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1103 helix: 1.49 (0.26), residues: 395 sheet: -0.17 (0.30), residues: 283 loop : -0.07 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 10 TYR 0.015 0.002 TYR A 318 PHE 0.024 0.002 PHE A 208 TRP 0.018 0.002 TRP B 297 HIS 0.006 0.001 HIS C 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8590) covalent geometry : angle 0.63805 / 0.34 (11694) SS BOND : bond 0.00216 / 0.11 ( 3) SS BOND : angle 1.21434 / 0.52 ( 6) hydrogen bonds : bond 0.04280 / 2.86 ( 455) hydrogen bonds : angle 5.49858 / 3.81 ( 1284) link_TRANS : bond 0.00247 / 0.13 ( 1) link_TRANS : angle 1.21603 / 0.61 ( 3) *********************** 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 215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.8096 (p90) cc_final: 0.7724 (p90) REVERT: A 309 GLU cc_start: 0.8768 (pm20) cc_final: 0.8457 (pm20) REVERT: A 330 GLU cc_start: 0.7958 (tp30) cc_final: 0.7533 (tp30) REVERT: B 234 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: H 184 SER cc_start: 0.9356 (p) cc_final: 0.9058 (m) REVERT: C 34 PHE cc_start: 0.8637 (t80) cc_final: 0.8150 (t80) REVERT: C 92 ARG cc_start: 0.7101 (tpt-90) cc_final: 0.5885 (tmm-80) REVERT: C 160 TYR cc_start: 0.6780 (t80) cc_final: 0.6402 (t80) REVERT: C 355 CYS cc_start: 0.8388 (m) cc_final: 0.7911 (m) REVERT: C 414 MET cc_start: 0.7859 (ppp) cc_final: 0.7619 (ppp) REVERT: C 418 HIS cc_start: 0.7629 (m90) cc_final: 0.7405 (m90) outliers start: 14 outliers final: 8 residues processed: 210 average time/residue: 0.0953 time to fit residues: 27.0242 Evaluate side-chains 187 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 178 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 C residue 69 LEU Chi-restraints excluded: chain C residue 174 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 HIS H 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.188332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144903 restraints weight = 10869.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144243 restraints weight = 7365.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145707 restraints weight = 6023.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147074 restraints weight = 4650.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.147480 restraints weight = 4078.161| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8594 Z= 0.159 Angle : 0.619 7.389 11703 Z= 0.324 Chirality : 0.044 0.157 1350 Planarity : 0.004 0.048 1494 Dihedral : 5.169 58.631 1210 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.63 % Allowed : 15.63 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1103 helix: 1.61 (0.26), residues: 405 sheet: -0.23 (0.30), residues: 277 loop : -0.02 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 18 TYR 0.015 0.002 TYR A 318 PHE 0.033 0.002 PHE A 208 TRP 0.016 0.002 TRP B 63 HIS 0.007 0.001 HIS C 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 8590) covalent geometry : angle 0.61852 / 0.32 (11694) SS BOND : bond 0.00875 / 0.43 ( 3) SS BOND : angle 0.87866 / 0.38 ( 6) hydrogen bonds : bond 0.03903 / 2.61 ( 455) hydrogen bonds : angle 5.24592 / 3.64 ( 1284) link_TRANS : bond 0.00226 / 0.12 ( 1) link_TRANS : angle 1.12539 / 0.57 ( 3) *********************** 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 211 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8219 (ptm160) cc_final: 0.7806 (ttp-170) REVERT: A 309 GLU cc_start: 0.8767 (pm20) cc_final: 0.8497 (pm20) REVERT: B 168 LEU cc_start: 0.8813 (tp) cc_final: 0.8373 (tt) REVERT: B 234 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: H 140 MET cc_start: 0.7942 (mmm) cc_final: 0.7664 (mmm) REVERT: H 184 SER cc_start: 0.9447 (p) cc_final: 0.9120 (m) REVERT: C 92 ARG cc_start: 0.7059 (tpt-90) cc_final: 0.5847 (tmm-80) REVERT: C 107 PHE cc_start: 0.6261 (m-80) cc_final: 0.5941 (m-80) REVERT: C 160 TYR cc_start: 0.6776 (t80) cc_final: 0.6293 (t80) REVERT: C 355 CYS cc_start: 0.8502 (m) cc_final: 0.8080 (m) REVERT: C 418 HIS cc_start: 0.7566 (m90) cc_final: 0.7344 (m90) REVERT: D 6 MET cc_start: 0.8295 (tpp) cc_final: 0.7984 (tpp) outliers start: 22 outliers final: 15 residues processed: 197 average time/residue: 0.0907 time to fit residues: 24.5655 Evaluate side-chains 187 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 H residue 210 THR Chi-restraints excluded: chain C residue 69 LEU 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 105 optimal weight: 0.0470 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN 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 = 0.4160 r_free = 0.4160 target = 0.188413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145659 restraints weight = 10942.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145544 restraints weight = 5727.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148140 restraints weight = 4505.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149110 restraints weight = 3680.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149601 restraints weight = 3402.547| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2461 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= 0.152 Angle : 0.599 8.629 11703 Z= 0.311 Chirality : 0.044 0.365 1350 Planarity : 0.004 0.050 1494 Dihedral : 5.016 59.921 1210 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.46 % Allowed : 16.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1103 helix: 1.74 (0.26), residues: 405 sheet: -0.34 (0.30), residues: 276 loop : 0.00 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 18 TYR 0.012 0.001 TYR H 59 PHE 0.024 0.002 PHE A 340 TRP 0.015 0.002 TRP C 88 HIS 0.007 0.001 HIS C 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 8590) covalent geometry : angle 0.59834 / 0.31 (11694) SS BOND : bond 0.00193 / 0.10 ( 3) SS BOND : angle 0.89263 / 0.38 ( 6) hydrogen bonds : bond 0.03620 / 2.41 ( 455) hydrogen bonds : angle 5.09778 / 3.55 ( 1284) link_TRANS : bond 0.00225 / 0.12 ( 1) link_TRANS : angle 0.93354 / 0.47 ( 3) *********************** 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 221 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8754 (pm20) cc_final: 0.8503 (pm20) REVERT: B 168 LEU cc_start: 0.8797 (tp) cc_final: 0.8360 (tt) REVERT: B 198 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7567 (pp) REVERT: B 234 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: B 292 PHE cc_start: 0.8727 (m-10) cc_final: 0.8237 (m-10) REVERT: G 27 ARG cc_start: 0.8414 (ttm110) cc_final: 0.7496 (ttm110) REVERT: H 140 MET cc_start: 0.8072 (mmm) cc_final: 0.7844 (mmm) REVERT: H 184 SER cc_start: 0.9439 (p) cc_final: 0.9066 (m) REVERT: C 107 PHE cc_start: 0.6206 (m-80) cc_final: 0.5971 (m-80) REVERT: C 355 CYS cc_start: 0.8532 (m) cc_final: 0.8106 (m) outliers start: 29 outliers final: 19 residues processed: 209 average time/residue: 0.0822 time to fit residues: 23.8071 Evaluate side-chains 196 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4157 r_free = 0.4157 target = 0.185798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142941 restraints weight = 11359.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141195 restraints weight = 8258.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144087 restraints weight = 6285.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145374 restraints weight = 4592.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145976 restraints weight = 3976.476| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8594 Z= 0.196 Angle : 0.651 10.667 11703 Z= 0.337 Chirality : 0.045 0.256 1350 Planarity : 0.004 0.052 1494 Dihedral : 4.975 59.511 1208 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.53 % Allowed : 17.30 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1103 helix: 1.66 (0.26), residues: 402 sheet: -0.48 (0.30), residues: 276 loop : -0.09 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 18 TYR 0.012 0.002 TYR H 190 PHE 0.022 0.002 PHE C 34 TRP 0.016 0.002 TRP C 88 HIS 0.009 0.002 HIS C 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 8590) covalent geometry : angle 0.65043 / 0.34 (11694) SS BOND : bond 0.00264 / 0.14 ( 3) SS BOND : angle 0.80103 / 0.35 ( 6) hydrogen bonds : bond 0.03757 / 2.49 ( 455) hydrogen bonds : angle 5.26907 / 3.66 ( 1284) link_TRANS : bond 0.00129 / 0.07 ( 1) link_TRANS : angle 0.81807 / 0.41 ( 3) *********************** 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 228 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8727 (pm20) cc_final: 0.8475 (pm20) REVERT: A 330 GLU cc_start: 0.7824 (tp30) cc_final: 0.7503 (tp30) REVERT: B 168 LEU cc_start: 0.8831 (tp) cc_final: 0.8365 (tt) REVERT: B 198 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7706 (pp) REVERT: B 234 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: B 292 PHE cc_start: 0.8637 (m-10) cc_final: 0.8303 (m-10) REVERT: G 27 ARG cc_start: 0.8468 (ttm110) cc_final: 0.7578 (ttm110) REVERT: C 107 PHE cc_start: 0.6253 (m-80) cc_final: 0.5651 (m-80) REVERT: D 6 MET cc_start: 0.8279 (tpp) cc_final: 0.7837 (tpp) outliers start: 38 outliers final: 26 residues processed: 213 average time/residue: 0.0920 time to fit residues: 27.2059 Evaluate side-chains 206 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 294 CYS 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 116 THR Chi-restraints excluded: chain H residue 141 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 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 103 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN 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 = 0.4146 r_free = 0.4146 target = 0.186820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143300 restraints weight = 10872.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142660 restraints weight = 6620.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144538 restraints weight = 5492.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145969 restraints weight = 4223.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147034 restraints weight = 3570.963| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8594 Z= 0.163 Angle : 0.619 8.085 11703 Z= 0.322 Chirality : 0.044 0.252 1350 Planarity : 0.004 0.055 1494 Dihedral : 4.818 59.643 1208 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.58 % Allowed : 18.50 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1103 helix: 1.67 (0.26), residues: 404 sheet: -0.50 (0.31), residues: 262 loop : -0.22 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 161 TYR 0.016 0.002 TYR A 318 PHE 0.030 0.002 PHE A 340 TRP 0.017 0.001 TRP C 88 HIS 0.008 0.001 HIS C 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 8590) covalent geometry : angle 0.61866 / 0.32 (11694) SS BOND : bond 0.00182 / 0.09 ( 3) SS BOND : angle 0.77054 / 0.33 ( 6) hydrogen bonds : bond 0.03632 / 2.41 ( 455) hydrogen bonds : angle 5.13804 / 3.58 ( 1284) link_TRANS : bond 0.00233 / 0.12 ( 1) link_TRANS : angle 1.02474 / 0.51 ( 3) *********************** 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 215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8788 (pm20) cc_final: 0.8508 (pm20) REVERT: A 330 GLU cc_start: 0.7842 (tp30) cc_final: 0.7504 (tp30) REVERT: B 17 GLN cc_start: 0.8181 (pt0) cc_final: 0.7771 (mm-40) REVERT: B 168 LEU cc_start: 0.8881 (tp) cc_final: 0.8417 (tt) REVERT: B 198 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7605 (pp) REVERT: B 234 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: B 292 PHE cc_start: 0.8712 (m-10) cc_final: 0.8239 (m-10) REVERT: G 27 ARG cc_start: 0.8516 (ttm110) cc_final: 0.7547 (ttm110) REVERT: H 184 SER cc_start: 0.9433 (p) cc_final: 0.8981 (m) REVERT: D 6 MET cc_start: 0.8368 (tpp) cc_final: 0.8119 (tpp) outliers start: 30 outliers final: 22 residues processed: 201 average time/residue: 0.0913 time to fit residues: 25.7892 Evaluate side-chains 199 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 141 THR Chi-restraints excluded: chain H residue 172 THR 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 Chi-restraints excluded: chain C residue 373 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 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 = 0.4150 r_free = 0.4150 target = 0.187107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143797 restraints weight = 10905.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145957 restraints weight = 7226.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148451 restraints weight = 5002.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148899 restraints weight = 3644.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149442 restraints weight = 3427.129| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8594 Z= 0.160 Angle : 0.632 9.063 11703 Z= 0.324 Chirality : 0.044 0.262 1350 Planarity : 0.004 0.060 1494 Dihedral : 4.817 59.196 1208 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.94 % Allowed : 18.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.26), residues: 1103 helix: 1.77 (0.26), residues: 402 sheet: -0.51 (0.31), residues: 262 loop : -0.20 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 340 TYR 0.014 0.001 TYR A 318 PHE 0.024 0.002 PHE A 208 TRP 0.020 0.001 TRP C 88 HIS 0.008 0.001 HIS C 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 8590) covalent geometry : angle 0.63150 / 0.32 (11694) SS BOND : bond 0.00184 / 0.10 ( 3) SS BOND : angle 0.73551 / 0.31 ( 6) hydrogen bonds : bond 0.03580 / 2.37 ( 455) hydrogen bonds : angle 5.07615 / 3.55 ( 1284) link_TRANS : bond 0.00196 / 0.10 ( 1) link_TRANS : angle 0.95806 / 0.48 ( 3) *********************** 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 219 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.258 Fit side-chains REVERT: A 309 GLU cc_start: 0.8704 (pm20) cc_final: 0.8486 (pm20) REVERT: B 17 GLN cc_start: 0.8004 (pt0) cc_final: 0.7629 (mm-40) REVERT: B 168 LEU cc_start: 0.8894 (tp) cc_final: 0.8397 (tt) REVERT: B 198 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7550 (pp) REVERT: B 234 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: B 292 PHE cc_start: 0.8756 (m-10) cc_final: 0.8252 (m-10) REVERT: H 184 SER cc_start: 0.9451 (p) cc_final: 0.8981 (m) REVERT: C 107 PHE cc_start: 0.6235 (m-80) cc_final: 0.5829 (m-80) REVERT: C 375 THR cc_start: 0.7997 (m) cc_final: 0.7671 (m) REVERT: D 6 MET cc_start: 0.8398 (tpp) cc_final: 0.7990 (tpp) outliers start: 33 outliers final: 28 residues processed: 204 average time/residue: 0.0794 time to fit residues: 22.6629 Evaluate side-chains 203 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 69 THR Chi-restraints excluded: chain H residue 141 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 159 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 373 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 chunk 41 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 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 = 0.4177 r_free = 0.4177 target = 0.189931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141031 restraints weight = 10790.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145592 restraints weight = 6439.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148870 restraints weight = 4555.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.151090 restraints weight = 3580.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.152308 restraints weight = 3035.849| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3291 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= 0.130 Angle : 0.631 11.125 11703 Z= 0.323 Chirality : 0.044 0.299 1350 Planarity : 0.004 0.067 1494 Dihedral : 4.671 58.521 1208 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.86 % Allowed : 20.17 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1103 helix: 1.83 (0.26), residues: 402 sheet: -0.54 (0.31), residues: 263 loop : -0.08 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.017 0.001 TYR C 160 PHE 0.026 0.002 PHE A 208 TRP 0.022 0.001 TRP C 88 HIS 0.007 0.001 HIS C 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8590) covalent geometry : angle 0.63119 / 0.32 (11694) SS BOND : bond 0.00138 / 0.07 ( 3) SS BOND : angle 0.85591 / 0.37 ( 6) hydrogen bonds : bond 0.03498 / 2.29 ( 455) hydrogen bonds : angle 4.91329 / 3.45 ( 1284) link_TRANS : bond 0.00227 / 0.12 ( 1) link_TRANS : angle 0.97939 / 0.49 ( 3) *********************** 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 210 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.311 Fit side-chains REVERT: B 17 GLN cc_start: 0.7988 (pt0) cc_final: 0.7693 (mm-40) REVERT: B 168 LEU cc_start: 0.8877 (tp) cc_final: 0.8396 (tt) REVERT: B 198 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7539 (pp) REVERT: B 234 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: B 292 PHE cc_start: 0.8603 (m-10) cc_final: 0.8267 (m-10) REVERT: H 18 ARG cc_start: 0.7543 (ttt180) cc_final: 0.7322 (ttt180) REVERT: H 184 SER cc_start: 0.9456 (p) cc_final: 0.9000 (m) REVERT: C 107 PHE cc_start: 0.6082 (m-80) cc_final: 0.5617 (m-80) REVERT: C 375 THR cc_start: 0.7878 (m) cc_final: 0.7583 (m) REVERT: D 6 MET cc_start: 0.8472 (tpp) cc_final: 0.7936 (tpp) outliers start: 24 outliers final: 18 residues processed: 199 average time/residue: 0.0747 time to fit residues: 20.8208 Evaluate side-chains 196 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 29 THR Chi-restraints excluded: chain B residue 190 LEU 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 H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 373 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9435 > 50: distance: 94 - 218: 17.306 distance: 97 - 215: 21.414 distance: 105 - 206: 29.859 distance: 108 - 203: 10.983 distance: 159 - 164: 8.912 distance: 164 - 165: 5.714 distance: 165 - 166: 6.861 distance: 165 - 168: 12.317 distance: 166 - 167: 5.092 distance: 166 - 172: 15.274 distance: 168 - 169: 15.862 distance: 169 - 170: 11.283 distance: 169 - 171: 19.432 distance: 172 - 173: 8.142 distance: 173 - 174: 14.515 distance: 173 - 176: 11.440 distance: 174 - 175: 24.042 distance: 174 - 179: 10.321 distance: 176 - 177: 9.763 distance: 176 - 178: 17.972 distance: 179 - 180: 8.578 distance: 180 - 181: 16.592 distance: 180 - 183: 8.045 distance: 181 - 182: 9.841 distance: 181 - 190: 14.918 distance: 183 - 184: 4.780 distance: 184 - 185: 8.991 distance: 184 - 186: 13.079 distance: 185 - 187: 7.039 distance: 186 - 188: 8.073 distance: 187 - 189: 10.975 distance: 188 - 189: 12.829 distance: 190 - 191: 9.132 distance: 191 - 192: 8.970 distance: 192 - 193: 21.992 distance: 192 - 194: 7.185 distance: 194 - 195: 11.725 distance: 195 - 196: 8.672 distance: 195 - 198: 11.076 distance: 196 - 197: 16.487 distance: 196 - 199: 12.446 distance: 199 - 200: 14.722 distance: 200 - 201: 6.164 distance: 201 - 202: 18.747 distance: 201 - 203: 21.619 distance: 203 - 204: 8.603 distance: 204 - 205: 11.479 distance: 204 - 207: 16.614 distance: 205 - 206: 12.358 distance: 205 - 210: 18.352 distance: 207 - 208: 17.026 distance: 207 - 209: 10.225 distance: 210 - 211: 12.511 distance: 211 - 212: 26.012 distance: 211 - 214: 27.594 distance: 212 - 213: 7.949 distance: 212 - 215: 21.609 distance: 215 - 216: 7.843 distance: 216 - 217: 9.021 distance: 216 - 219: 24.041 distance: 217 - 218: 22.048 distance: 217 - 220: 4.051 distance: 220 - 221: 5.032 distance: 221 - 222: 6.909 distance: 221 - 224: 6.568 distance: 222 - 223: 19.598 distance: 222 - 229: 4.336 distance: 224 - 225: 3.096 distance: 225 - 226: 9.335 distance: 226 - 227: 5.275 distance: 226 - 228: 3.191