Starting phenix.real_space_refine on Wed Feb 12 10:24:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dh5_30678/02_2025/7dh5_30678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dh5_30678/02_2025/7dh5_30678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dh5_30678/02_2025/7dh5_30678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dh5_30678/02_2025/7dh5_30678.map" model { file = "/net/cci-nas-00/data/ceres_data/7dh5_30678/02_2025/7dh5_30678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dh5_30678/02_2025/7dh5_30678.cif" } resolution = 3.16 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= 0.009 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 47 5.16 5 C 4975 2.51 5 N 1383 2.21 5 O 1445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7850 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2052 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'H6U': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.69, per 1000 atoms: 0.60 Number of scatterers: 7850 At special positions: 0 Unit cell: (98.5625, 79.8875, 132.8, 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 47 16.00 O 1445 8.00 N 1383 7.00 C 4975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 41.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.649A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.508A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.249A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.957A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.614A pdb=" N ARG A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.638A pdb=" N ASP A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 371 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.693A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.627A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.536A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 64 Processing helix chain 'R' and resid 72 through 90 Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 106 through 141 removed outlier: 3.564A pdb=" N THR R 122 " --> pdb=" O VAL R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 170 Processing helix chain 'R' and resid 188 through 192 Processing helix chain 'R' and resid 201 through 213 Processing helix chain 'R' and resid 213 through 241 Processing helix chain 'R' and resid 289 through 318 removed outlier: 4.314A pdb=" N CYS R 304 " --> pdb=" O THR R 300 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 324 through 346 Proline residue: R 343 - end of helix removed outlier: 3.560A pdb=" N TYR R 346 " --> pdb=" O ASN R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.236A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.667A 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: 3.672A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.866A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 150 removed outlier: 3.652A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.521A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.010A 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: 3.676A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.659A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.648A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'N' and resid 49 through 50 removed outlier: 3.600A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1119 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: 2.32 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1277 1.31 - 1.44: 2179 1.44 - 1.56: 4488 1.56 - 1.69: 2 1.69 - 1.81: 61 Bond restraints: 8007 Sorted by residual: bond pdb=" C27 H6U R 401 " pdb=" S28 H6U R 401 " ideal model delta sigma weight residual 1.731 1.589 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C02 H6U R 401 " pdb=" S28 H6U R 401 " ideal model delta sigma weight residual 1.742 1.616 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C06 H6U R 401 " pdb=" N08 H6U R 401 " ideal model delta sigma weight residual 1.353 1.464 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C ARG N 98 " pdb=" N CYS N 99 " ideal model delta sigma weight residual 1.333 1.209 0.124 2.74e-02 1.33e+03 2.03e+01 bond pdb=" C02 H6U R 401 " pdb=" N01 H6U R 401 " ideal model delta sigma weight residual 1.348 1.438 -0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 8002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 10653 2.28 - 4.56: 199 4.56 - 6.84: 29 6.84 - 9.12: 2 9.12 - 11.40: 2 Bond angle restraints: 10885 Sorted by residual: angle pdb=" N ILE A 365 " pdb=" CA ILE A 365 " pdb=" C ILE A 365 " ideal model delta sigma weight residual 112.35 106.61 5.74 1.41e+00 5.03e-01 1.66e+01 angle pdb=" C LEU R 221 " pdb=" N PHE R 222 " pdb=" CA PHE R 222 " ideal model delta sigma weight residual 120.31 114.26 6.05 1.52e+00 4.33e-01 1.58e+01 angle pdb=" N VAL R 37 " pdb=" CA VAL R 37 " pdb=" C VAL R 37 " ideal model delta sigma weight residual 113.16 107.84 5.32 1.49e+00 4.50e-01 1.27e+01 angle pdb=" C02 H6U R 401 " pdb=" S28 H6U R 401 " pdb=" C27 H6U R 401 " ideal model delta sigma weight residual 89.03 98.94 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C ARG N 98 " pdb=" N CYS N 99 " pdb=" CA CYS N 99 " ideal model delta sigma weight residual 122.15 110.75 11.40 3.47e+00 8.31e-02 1.08e+01 ... (remaining 10880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4310 18.01 - 36.03: 376 36.03 - 54.04: 59 54.04 - 72.06: 14 72.06 - 90.07: 5 Dihedral angle restraints: 4764 sinusoidal: 1788 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 158.35 -65.35 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CA LEU A 281 " pdb=" C LEU A 281 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta harmonic sigma weight residual 180.00 -146.23 -33.77 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CB CYS R 189 " pdb=" SG CYS R 189 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual -86.00 -122.50 36.50 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 4761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 708 0.036 - 0.072: 386 0.072 - 0.109: 124 0.109 - 0.145: 37 0.145 - 0.181: 3 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CA PHE R 222 " pdb=" N PHE R 222 " pdb=" C PHE R 222 " pdb=" CB PHE R 222 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 1255 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE N 108 " -0.023 2.00e-02 2.50e+03 2.69e-02 1.26e+01 pdb=" CG PHE N 108 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE N 108 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE N 108 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE N 108 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE N 108 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE N 108 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 308 " -0.018 2.00e-02 2.50e+03 1.35e-02 3.21e+00 pdb=" CG PHE R 308 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE R 308 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 308 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE R 308 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 308 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 321 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO A 322 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.024 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 83 2.58 - 3.16: 6554 3.16 - 3.74: 12116 3.74 - 4.32: 17285 4.32 - 4.90: 29426 Nonbonded interactions: 65464 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.005 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.066 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP R 117 " pdb=" N VAL R 118 " model vdw 2.245 3.120 ... (remaining 65459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.260 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.008 0.142 8007 Z= 0.550 Angle : 0.798 11.404 10885 Z= 0.442 Chirality : 0.049 0.181 1258 Planarity : 0.005 0.044 1394 Dihedral : 14.096 90.073 2826 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.78 (0.22), residues: 1011 helix: -1.82 (0.22), residues: 378 sheet: -3.37 (0.28), residues: 201 loop : -2.54 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 99 HIS 0.012 0.002 HIS A 347 PHE 0.061 0.003 PHE N 108 TYR 0.017 0.002 TYR B 59 ARG 0.012 0.001 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8301 (tttm) cc_final: 0.7973 (tttt) REVERT: A 323 ARG cc_start: 0.6958 (mtp180) cc_final: 0.6752 (mtm180) REVERT: B 61 MET cc_start: 0.8785 (ppp) cc_final: 0.8464 (ppp) REVERT: B 111 TYR cc_start: 0.8725 (m-80) cc_final: 0.8494 (m-80) REVERT: B 219 ARG cc_start: 0.7515 (mmt-90) cc_final: 0.7147 (mtp-110) REVERT: R 238 LEU cc_start: 0.8186 (tt) cc_final: 0.7864 (tp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2795 time to fit residues: 48.7906 Evaluate side-chains 115 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 213 GLN A 261 ASN A 268 ASN B 88 ASN B 239 ASN B 268 ASN N 1 GLN N 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117554 restraints weight = 8678.687| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.50 r_work: 0.3113 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8007 Z= 0.183 Angle : 0.600 6.984 10885 Z= 0.317 Chirality : 0.043 0.193 1258 Planarity : 0.005 0.058 1394 Dihedral : 6.034 74.438 1126 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.72 % Allowed : 12.01 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.07 (0.25), residues: 1011 helix: 0.14 (0.26), residues: 377 sheet: -2.75 (0.31), residues: 203 loop : -1.97 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.035 0.002 PHE R 222 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.812 Fit side-chains REVERT: A 16 GLU cc_start: 0.7560 (mp0) cc_final: 0.7166 (mp0) REVERT: A 17 LYS cc_start: 0.8541 (tttm) cc_final: 0.8255 (tttt) REVERT: A 209 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6893 (mm-30) REVERT: A 249 ASP cc_start: 0.8107 (p0) cc_final: 0.7878 (p0) REVERT: B 33 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.6976 (mp) REVERT: B 219 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.7611 (mtp-110) REVERT: R 238 LEU cc_start: 0.8330 (tt) cc_final: 0.8092 (tp) REVERT: R 242 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8416 (tt) outliers start: 14 outliers final: 8 residues processed: 141 average time/residue: 0.2531 time to fit residues: 45.6081 Evaluate side-chains 124 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117985 restraints weight = 8786.247| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.53 r_work: 0.3170 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8007 Z= 0.166 Angle : 0.547 7.622 10885 Z= 0.287 Chirality : 0.042 0.192 1258 Planarity : 0.004 0.048 1394 Dihedral : 5.479 71.654 1126 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.70 % Allowed : 14.34 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 1011 helix: 0.98 (0.27), residues: 377 sheet: -2.43 (0.30), residues: 205 loop : -1.71 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.030 0.002 PHE R 222 TYR 0.015 0.001 TYR B 264 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.841 Fit side-chains REVERT: A 16 GLU cc_start: 0.7515 (mp0) cc_final: 0.7114 (mp0) REVERT: A 17 LYS cc_start: 0.8511 (tttm) cc_final: 0.8252 (tttt) REVERT: A 299 GLU cc_start: 0.8164 (pm20) cc_final: 0.7947 (pm20) REVERT: B 33 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.6865 (mp) REVERT: B 219 ARG cc_start: 0.7856 (mmt-90) cc_final: 0.7646 (mtp-110) REVERT: R 238 LEU cc_start: 0.8412 (tt) cc_final: 0.8189 (tp) REVERT: R 241 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7196 (mt-10) REVERT: R 242 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8424 (tt) outliers start: 22 outliers final: 15 residues processed: 140 average time/residue: 0.2537 time to fit residues: 45.6118 Evaluate side-chains 132 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 303 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 0.0870 chunk 57 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 0.0870 chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 69 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.144956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115082 restraints weight = 8784.478| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.51 r_work: 0.3132 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8007 Z= 0.263 Angle : 0.574 10.255 10885 Z= 0.299 Chirality : 0.043 0.155 1258 Planarity : 0.004 0.045 1394 Dihedral : 5.608 70.367 1126 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.43 % Allowed : 16.05 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1011 helix: 1.21 (0.27), residues: 372 sheet: -2.00 (0.31), residues: 219 loop : -1.50 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.007 0.001 HIS A 347 PHE 0.031 0.002 PHE R 222 TYR 0.015 0.001 TYR A 37 ARG 0.004 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.844 Fit side-chains REVERT: A 16 GLU cc_start: 0.7521 (mp0) cc_final: 0.7089 (mp0) REVERT: A 17 LYS cc_start: 0.8521 (tttm) cc_final: 0.8276 (tttt) REVERT: A 307 ARG cc_start: 0.8143 (ptp-110) cc_final: 0.7783 (mtm-85) REVERT: B 33 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.6867 (mp) REVERT: B 217 MET cc_start: 0.8084 (ttt) cc_final: 0.7638 (ppp) REVERT: B 219 ARG cc_start: 0.7927 (mmt-90) cc_final: 0.7668 (mtp-110) REVERT: B 234 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8495 (m-80) REVERT: N 94 TYR cc_start: 0.8831 (m-80) cc_final: 0.8539 (m-80) REVERT: N 108 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8529 (t80) REVERT: R 238 LEU cc_start: 0.8400 (tt) cc_final: 0.8197 (tp) REVERT: R 242 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8436 (tt) REVERT: R 357 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7252 (ttp80) outliers start: 28 outliers final: 20 residues processed: 138 average time/residue: 0.2473 time to fit residues: 44.0328 Evaluate side-chains 139 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 0.0270 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117822 restraints weight = 8607.480| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.50 r_work: 0.3167 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8007 Z= 0.169 Angle : 0.535 10.995 10885 Z= 0.277 Chirality : 0.041 0.157 1258 Planarity : 0.004 0.043 1394 Dihedral : 5.364 69.226 1126 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.04 % Allowed : 16.91 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 1011 helix: 1.47 (0.27), residues: 373 sheet: -2.06 (0.31), residues: 221 loop : -1.30 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.027 0.001 PHE R 222 TYR 0.012 0.001 TYR A 37 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.843 Fit side-chains REVERT: A 16 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: A 17 LYS cc_start: 0.8482 (tttm) cc_final: 0.8251 (tttt) REVERT: A 307 ARG cc_start: 0.8104 (ptp-110) cc_final: 0.7732 (mtm-85) REVERT: B 33 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6881 (mp) REVERT: B 153 ASP cc_start: 0.8443 (m-30) cc_final: 0.8163 (m-30) REVERT: B 219 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7614 (mtp-110) REVERT: B 234 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: N 94 TYR cc_start: 0.8772 (m-80) cc_final: 0.8542 (m-80) REVERT: R 242 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8391 (tt) REVERT: R 357 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7249 (ttp80) outliers start: 33 outliers final: 22 residues processed: 146 average time/residue: 0.2378 time to fit residues: 45.2571 Evaluate side-chains 142 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 220 MET Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.115493 restraints weight = 8741.971| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.51 r_work: 0.3161 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8007 Z= 0.252 Angle : 0.574 11.456 10885 Z= 0.296 Chirality : 0.043 0.172 1258 Planarity : 0.004 0.042 1394 Dihedral : 5.510 68.609 1126 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.29 % Allowed : 17.52 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.27), residues: 1011 helix: 1.55 (0.27), residues: 373 sheet: -2.03 (0.31), residues: 225 loop : -1.15 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.007 0.001 HIS A 347 PHE 0.028 0.002 PHE R 222 TYR 0.017 0.001 TYR R 346 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.824 Fit side-chains REVERT: A 16 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: A 17 LYS cc_start: 0.8488 (tttm) cc_final: 0.8262 (tttt) REVERT: B 33 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.6929 (mp) REVERT: B 219 ARG cc_start: 0.7904 (mmt-90) cc_final: 0.7652 (mtp-110) REVERT: B 234 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8456 (m-80) REVERT: R 64 ARG cc_start: 0.7860 (ptp-170) cc_final: 0.7647 (ptp-170) REVERT: R 242 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8420 (tt) REVERT: R 357 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7267 (ttp80) outliers start: 35 outliers final: 23 residues processed: 138 average time/residue: 0.2406 time to fit residues: 43.0043 Evaluate side-chains 137 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 0.3980 chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118956 restraints weight = 8631.800| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.51 r_work: 0.3195 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8007 Z= 0.157 Angle : 0.533 11.917 10885 Z= 0.274 Chirality : 0.041 0.168 1258 Planarity : 0.004 0.041 1394 Dihedral : 5.224 67.734 1126 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.80 % Allowed : 17.65 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.27), residues: 1011 helix: 1.74 (0.27), residues: 377 sheet: -1.90 (0.32), residues: 224 loop : -1.18 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.025 0.001 PHE R 222 TYR 0.014 0.001 TYR B 264 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.844 Fit side-chains REVERT: A 16 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: A 17 LYS cc_start: 0.8478 (tttm) cc_final: 0.8264 (tttt) REVERT: B 33 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6854 (mp) REVERT: B 219 ARG cc_start: 0.7888 (mmt-90) cc_final: 0.7609 (mtp-110) REVERT: B 234 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: N 98 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7890 (ppt170) REVERT: R 148 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7803 (tt) REVERT: R 242 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8305 (tt) REVERT: R 357 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7241 (ttp80) outliers start: 31 outliers final: 19 residues processed: 139 average time/residue: 0.2403 time to fit residues: 43.4707 Evaluate side-chains 138 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.147625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117754 restraints weight = 8631.694| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.52 r_work: 0.3164 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8007 Z= 0.193 Angle : 0.540 12.116 10885 Z= 0.277 Chirality : 0.042 0.183 1258 Planarity : 0.004 0.041 1394 Dihedral : 5.262 67.145 1126 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.78 % Allowed : 17.16 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 1011 helix: 1.86 (0.27), residues: 375 sheet: -1.87 (0.32), residues: 222 loop : -1.08 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.024 0.001 PHE R 222 TYR 0.014 0.001 TYR R 346 ARG 0.007 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.947 Fit side-chains REVERT: A 17 LYS cc_start: 0.8466 (tttm) cc_final: 0.8256 (tttt) REVERT: A 307 ARG cc_start: 0.8128 (ptp-110) cc_final: 0.7791 (mtm-85) REVERT: B 33 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.6915 (mp) REVERT: B 153 ASP cc_start: 0.8377 (m-30) cc_final: 0.8164 (m-30) REVERT: B 219 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7671 (mtp-110) REVERT: B 234 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: N 98 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8015 (ppt170) REVERT: R 148 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7836 (tt) REVERT: R 242 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8255 (tt) REVERT: R 357 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7296 (ttp80) outliers start: 39 outliers final: 26 residues processed: 146 average time/residue: 0.2459 time to fit residues: 46.4457 Evaluate side-chains 148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 84 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.149527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119601 restraints weight = 8726.060| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.54 r_work: 0.3204 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8007 Z= 0.158 Angle : 0.528 12.381 10885 Z= 0.271 Chirality : 0.041 0.185 1258 Planarity : 0.004 0.040 1394 Dihedral : 5.107 66.286 1126 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.17 % Allowed : 17.89 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.27), residues: 1011 helix: 1.99 (0.27), residues: 377 sheet: -1.81 (0.31), residues: 228 loop : -1.01 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.023 0.001 PHE R 222 TYR 0.011 0.001 TYR A 37 ARG 0.006 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.906 Fit side-chains REVERT: A 16 GLU cc_start: 0.7493 (mp0) cc_final: 0.7266 (mp0) REVERT: A 17 LYS cc_start: 0.8484 (tttm) cc_final: 0.8272 (tttt) REVERT: A 307 ARG cc_start: 0.8107 (ptp-110) cc_final: 0.7763 (mtm-85) REVERT: B 33 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.6927 (mp) REVERT: B 234 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: N 98 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7973 (ppt170) REVERT: N 117 TYR cc_start: 0.8716 (m-80) cc_final: 0.8515 (m-80) REVERT: R 148 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7847 (tt) REVERT: R 242 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8237 (tt) REVERT: R 357 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7273 (ttp80) outliers start: 34 outliers final: 25 residues processed: 142 average time/residue: 0.2498 time to fit residues: 45.7200 Evaluate side-chains 143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 0.0020 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.151191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123254 restraints weight = 8601.478| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.66 r_work: 0.3244 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8007 Z= 0.144 Angle : 0.526 14.497 10885 Z= 0.268 Chirality : 0.041 0.173 1258 Planarity : 0.004 0.040 1394 Dihedral : 4.937 64.932 1126 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.55 % Allowed : 18.75 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.27), residues: 1011 helix: 2.09 (0.27), residues: 376 sheet: -1.66 (0.31), residues: 229 loop : -0.93 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.023 0.001 PHE R 222 TYR 0.010 0.001 TYR B 264 ARG 0.006 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.947 Fit side-chains REVERT: A 16 GLU cc_start: 0.7387 (mp0) cc_final: 0.7061 (mp0) REVERT: B 33 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6736 (mp) REVERT: B 234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8184 (m-80) REVERT: N 98 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8020 (ppt170) REVERT: R 134 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8451 (t70) REVERT: R 148 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7822 (tt) REVERT: R 242 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8244 (tt) REVERT: R 357 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7185 (ttp80) outliers start: 29 outliers final: 21 residues processed: 142 average time/residue: 0.2929 time to fit residues: 52.7921 Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 chunk 94 optimal weight: 6.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.150237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122284 restraints weight = 8652.771| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.65 r_work: 0.3233 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8007 Z= 0.171 Angle : 0.547 14.924 10885 Z= 0.277 Chirality : 0.042 0.172 1258 Planarity : 0.004 0.040 1394 Dihedral : 4.998 64.806 1126 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.68 % Allowed : 18.75 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.27), residues: 1011 helix: 2.06 (0.27), residues: 377 sheet: -1.62 (0.31), residues: 229 loop : -0.90 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.023 0.001 PHE R 222 TYR 0.011 0.001 TYR A 37 ARG 0.006 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4264.24 seconds wall clock time: 76 minutes 13.51 seconds (4573.51 seconds total)