Starting phenix.real_space_refine on Wed Mar 12 10:40:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dh5_30678/03_2025/7dh5_30678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dh5_30678/03_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_30678/03_2025/7dh5_30678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dh5_30678/03_2025/7dh5_30678.map" model { file = "/net/cci-nas-00/data/ceres_data/7dh5_30678/03_2025/7dh5_30678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dh5_30678/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.89, per 1000 atoms: 0.62 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: 2.03 Conformation dependent library (CDL) restraints added in 1.1 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: 0.88 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: 2.10 Time building geometry restraints manager: 2.38 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: 0.210 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.100 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- 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 : 0.859 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: 0.2849 time to fit residues: 49.8583 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 : 0.793 ------------------------------------------------------------------------------- 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: 3.39 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.852 Fit side-chains REVERT: A 16 GLU cc_start: 0.7555 (mp0) cc_final: 0.7161 (mp0) REVERT: A 17 LYS cc_start: 0.8532 (tttm) cc_final: 0.8242 (tttt) REVERT: A 209 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6897 (mm-30) REVERT: A 249 ASP cc_start: 0.8110 (p0) cc_final: 0.7879 (p0) REVERT: B 33 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.6968 (mp) REVERT: B 219 ARG cc_start: 0.7820 (mmt-90) cc_final: 0.7603 (mtp-110) REVERT: R 238 LEU cc_start: 0.8331 (tt) cc_final: 0.8094 (tp) REVERT: R 242 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8412 (tt) outliers start: 14 outliers final: 8 residues processed: 141 average time/residue: 0.2567 time to fit residues: 46.2086 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 : 0.774 ------------------------------------------------------------------------------- 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: 9.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.147339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117646 restraints weight = 8790.799| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.53 r_work: 0.3166 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1803 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= 0.170 Angle : 0.550 7.352 10885 Z= 0.288 Chirality : 0.042 0.197 1258 Planarity : 0.004 0.048 1394 Dihedral : 5.494 71.655 1126 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.70 % Allowed : 14.46 % Favored : 82.84 % 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: 0.97 (0.27), residues: 377 sheet: -2.42 (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 0.016 0.001 TYR B 264 ARG 0.004 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 : 0.789 Fit side-chains REVERT: A 16 GLU cc_start: 0.7491 (mp0) cc_final: 0.7086 (mp0) REVERT: A 17 LYS cc_start: 0.8493 (tttm) cc_final: 0.8234 (tttt) REVERT: A 299 GLU cc_start: 0.8170 (pm20) cc_final: 0.7954 (pm20) REVERT: B 33 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6819 (mp) REVERT: B 219 ARG cc_start: 0.7836 (mmt-90) cc_final: 0.7622 (mtp-110) REVERT: R 238 LEU cc_start: 0.8399 (tt) cc_final: 0.8184 (tp) REVERT: R 242 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8413 (tt) outliers start: 22 outliers final: 15 residues processed: 140 average time/residue: 0.2475 time to fit residues: 44.6210 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 : 0.787 ------------------------------------------------------------------------------- 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: 0.6980 chunk 57 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.146302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116671 restraints weight = 8753.268| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.51 r_work: 0.3164 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1901 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= 0.205 Angle : 0.551 10.677 10885 Z= 0.287 Chirality : 0.042 0.149 1258 Planarity : 0.004 0.044 1394 Dihedral : 5.470 69.877 1126 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.68 % Allowed : 15.44 % Favored : 80.88 % 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: -0.88 (0.27), residues: 1011 helix: 1.32 (0.27), residues: 372 sheet: -2.07 (0.31), residues: 224 loop : -1.41 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS A 347 PHE 0.029 0.002 PHE R 222 TYR 0.013 0.001 TYR A 37 ARG 0.003 0.000 ARG B 256 *********************** 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 148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.916 Fit side-chains REVERT: A 16 GLU cc_start: 0.7503 (mp0) cc_final: 0.7062 (mp0) REVERT: A 17 LYS cc_start: 0.8502 (tttm) cc_final: 0.8269 (tttt) REVERT: A 307 ARG cc_start: 0.8119 (ptp-110) cc_final: 0.7747 (mtm-85) REVERT: B 33 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.6930 (mp) REVERT: B 217 MET cc_start: 0.8066 (ttt) cc_final: 0.7639 (ppp) REVERT: B 234 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8484 (m-80) REVERT: N 94 TYR cc_start: 0.8803 (m-80) cc_final: 0.8524 (m-80) REVERT: N 108 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8479 (t80) REVERT: R 238 LEU cc_start: 0.8374 (tt) cc_final: 0.8159 (tp) REVERT: R 242 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8422 (tt) REVERT: R 357 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7257 (ttp80) outliers start: 30 outliers final: 19 residues processed: 140 average time/residue: 0.2444 time to fit residues: 44.4569 Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 309 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 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 220 MET 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: 0.0370 chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.147572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118218 restraints weight = 8605.914| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.50 r_work: 0.3180 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8007 Z= 0.184 Angle : 0.530 10.234 10885 Z= 0.275 Chirality : 0.042 0.157 1258 Planarity : 0.004 0.043 1394 Dihedral : 5.306 68.153 1126 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.04 % Allowed : 16.54 % Favored : 79.41 % 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: -0.64 (0.27), residues: 1011 helix: 1.56 (0.27), residues: 375 sheet: -2.02 (0.31), residues: 221 loop : -1.30 (0.30), residues: 415 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 0.027 0.001 PHE R 222 TYR 0.012 0.001 TYR A 37 ARG 0.005 0.000 ARG N 19 *********************** 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 155 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.793 Fit side-chains REVERT: A 16 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: A 17 LYS cc_start: 0.8498 (tttm) cc_final: 0.8277 (tttt) REVERT: A 295 LYS cc_start: 0.7499 (mmmt) cc_final: 0.7298 (mmmt) REVERT: A 307 ARG cc_start: 0.8132 (ptp-110) cc_final: 0.7739 (mtm-85) REVERT: B 33 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.6896 (mp) REVERT: B 153 ASP cc_start: 0.8381 (m-30) cc_final: 0.8096 (m-30) REVERT: B 217 MET cc_start: 0.7977 (ttt) cc_final: 0.7584 (ppp) REVERT: B 234 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: R 238 LEU cc_start: 0.8352 (tt) cc_final: 0.8134 (tp) REVERT: R 242 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8406 (tt) REVERT: R 357 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7241 (ttp80) outliers start: 33 outliers final: 22 residues processed: 147 average time/residue: 0.2335 time to fit residues: 44.7037 Evaluate side-chains 139 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 361 ASN 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114760 restraints weight = 8742.403| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.51 r_work: 0.3123 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8007 Z= 0.300 Angle : 0.583 11.342 10885 Z= 0.301 Chirality : 0.044 0.171 1258 Planarity : 0.004 0.043 1394 Dihedral : 5.523 68.315 1126 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.53 % Allowed : 17.28 % 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: -0.55 (0.27), residues: 1011 helix: 1.59 (0.27), residues: 372 sheet: -1.98 (0.32), residues: 225 loop : -1.16 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.008 0.001 HIS A 347 PHE 0.029 0.002 PHE R 222 TYR 0.016 0.002 TYR R 346 ARG 0.004 0.000 ARG N 98 *********************** 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 152 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.908 Fit side-chains REVERT: A 16 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: A 17 LYS cc_start: 0.8496 (tttm) cc_final: 0.8274 (tttt) REVERT: A 295 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7381 (mmmt) REVERT: B 33 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.6967 (mp) REVERT: B 153 ASP cc_start: 0.8432 (m-30) cc_final: 0.8215 (m-30) REVERT: B 234 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: R 148 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7833 (tt) REVERT: R 238 LEU cc_start: 0.8401 (tt) cc_final: 0.8159 (tp) REVERT: R 242 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8449 (tt) REVERT: R 357 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7279 (ttp80) outliers start: 37 outliers final: 25 residues processed: 143 average time/residue: 0.2383 time to fit residues: 44.6335 Evaluate side-chains 142 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain B residue 93 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 148 LEU 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: 3.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115273 restraints weight = 8722.103| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.50 r_work: 0.3097 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8007 Z= 0.269 Angle : 0.576 11.901 10885 Z= 0.296 Chirality : 0.043 0.182 1258 Planarity : 0.004 0.043 1394 Dihedral : 5.529 68.647 1126 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.66 % Allowed : 17.28 % 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: -0.45 (0.27), residues: 1011 helix: 1.64 (0.27), residues: 371 sheet: -1.90 (0.32), residues: 225 loop : -1.09 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.007 0.001 HIS A 347 PHE 0.027 0.002 PHE R 222 TYR 0.014 0.002 TYR A 37 ARG 0.004 0.000 ARG N 98 *********************** 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 151 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.721 Fit side-chains REVERT: A 16 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: A 17 LYS cc_start: 0.8484 (tttm) cc_final: 0.8270 (tttt) REVERT: A 295 LYS cc_start: 0.7742 (mmmt) cc_final: 0.7482 (mmmt) REVERT: A 307 ARG cc_start: 0.8148 (ptp-110) cc_final: 0.7823 (mtm-85) REVERT: B 33 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.6902 (mp) REVERT: B 234 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: N 98 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8224 (ppt170) REVERT: R 148 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7847 (tt) REVERT: R 238 LEU cc_start: 0.8385 (tt) cc_final: 0.8147 (tp) REVERT: R 242 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8390 (tt) REVERT: R 357 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7276 (ttp80) outliers start: 38 outliers final: 26 residues processed: 140 average time/residue: 0.2553 time to fit residues: 45.9080 Evaluate side-chains 143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 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 4 LEU Chi-restraints excluded: chain N residue 22 CYS 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 161 VAL Chi-restraints excluded: chain R residue 223 VAL 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: 1.9990 chunk 21 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.148300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118807 restraints weight = 8636.057| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.50 r_work: 0.3179 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8007 Z= 0.168 Angle : 0.535 12.272 10885 Z= 0.275 Chirality : 0.042 0.177 1258 Planarity : 0.004 0.041 1394 Dihedral : 5.220 67.795 1126 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.06 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: -0.29 (0.27), residues: 1011 helix: 1.82 (0.27), residues: 376 sheet: -1.83 (0.32), residues: 224 loop : -1.07 (0.31), residues: 411 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 0.024 0.001 PHE R 222 TYR 0.016 0.001 TYR B 264 ARG 0.004 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 148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.838 Fit side-chains REVERT: A 17 LYS cc_start: 0.8486 (tttm) cc_final: 0.8274 (tttt) REVERT: A 295 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7525 (mmmt) REVERT: A 307 ARG cc_start: 0.8127 (ptp-110) cc_final: 0.7796 (mtm-85) REVERT: B 33 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6862 (mp) REVERT: B 234 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: N 98 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7956 (ppt170) REVERT: R 148 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7815 (tt) REVERT: R 238 LEU cc_start: 0.8358 (tt) cc_final: 0.8126 (tp) REVERT: R 242 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8331 (tt) REVERT: R 357 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7224 (ttp80) outliers start: 30 outliers final: 19 residues processed: 142 average time/residue: 0.2458 time to fit residues: 44.8661 Evaluate side-chains 141 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP 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 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 242 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 0.0470 chunk 70 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.150819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121422 restraints weight = 8723.992| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.51 r_work: 0.3237 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2580 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= 0.145 Angle : 0.524 14.347 10885 Z= 0.267 Chirality : 0.041 0.187 1258 Planarity : 0.004 0.040 1394 Dihedral : 4.991 66.157 1126 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.68 % Allowed : 19.36 % Favored : 76.96 % 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: -0.08 (0.27), residues: 1011 helix: 2.03 (0.27), residues: 377 sheet: -1.75 (0.31), residues: 228 loop : -0.96 (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 0.022 0.001 PHE R 222 TYR 0.012 0.001 TYR B 264 ARG 0.009 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 147 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.866 Fit side-chains REVERT: A 17 LYS cc_start: 0.8510 (tttm) cc_final: 0.8310 (tttt) REVERT: A 295 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7539 (mmmt) REVERT: A 307 ARG cc_start: 0.8099 (ptp-110) cc_final: 0.7774 (mtm-85) REVERT: B 33 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.6809 (mp) REVERT: B 152 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7948 (tt) REVERT: B 234 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: R 148 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7856 (tt) REVERT: R 207 LEU cc_start: 0.7466 (mm) cc_final: 0.7017 (mm) REVERT: R 238 LEU cc_start: 0.8337 (tt) cc_final: 0.8110 (tp) REVERT: R 357 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7213 (ttp80) outliers start: 30 outliers final: 19 residues processed: 139 average time/residue: 0.2392 time to fit residues: 43.1759 Evaluate side-chains 134 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 152 LEU 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 269 ILE Chi-restraints excluded: chain B residue 318 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 148 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 220 MET Chi-restraints excluded: chain R residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109861 restraints weight = 8579.266| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.61 r_work: 0.3087 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2411 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= 0.269 Angle : 0.579 14.773 10885 Z= 0.294 Chirality : 0.043 0.186 1258 Planarity : 0.004 0.041 1394 Dihedral : 5.362 67.521 1126 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.31 % Allowed : 20.10 % Favored : 76.59 % 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: -0.08 (0.27), residues: 1011 helix: 1.96 (0.27), residues: 371 sheet: -1.74 (0.32), residues: 229 loop : -0.83 (0.32), residues: 411 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 0.025 0.002 PHE R 222 TYR 0.016 0.002 TYR A 37 ARG 0.007 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 144 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.830 Fit side-chains REVERT: A 16 GLU cc_start: 0.7438 (mp0) cc_final: 0.7176 (mp0) REVERT: A 17 LYS cc_start: 0.8418 (tttm) cc_final: 0.8198 (tttt) REVERT: A 295 LYS cc_start: 0.7763 (mmmt) cc_final: 0.7500 (mmmt) REVERT: A 307 ARG cc_start: 0.8100 (ptp-110) cc_final: 0.7746 (mtm-85) REVERT: B 33 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.6754 (mp) REVERT: B 152 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8144 (tt) REVERT: B 234 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: R 148 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7808 (tt) REVERT: R 238 LEU cc_start: 0.8254 (tt) cc_final: 0.8029 (tp) REVERT: R 357 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7198 (ttp80) outliers start: 27 outliers final: 18 residues processed: 138 average time/residue: 0.2523 time to fit residues: 45.5654 Evaluate side-chains 137 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 152 LEU 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 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 148 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.149128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.119324 restraints weight = 8658.340| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.53 r_work: 0.3212 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8007 Z= 0.167 Angle : 0.548 15.044 10885 Z= 0.278 Chirality : 0.042 0.171 1258 Planarity : 0.004 0.040 1394 Dihedral : 5.189 67.301 1126 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.43 % Allowed : 19.85 % Favored : 76.72 % 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: -0.07 (0.27), residues: 1011 helix: 2.02 (0.27), residues: 375 sheet: -1.68 (0.31), residues: 228 loop : -0.95 (0.32), residues: 408 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 0.023 0.001 PHE R 222 TYR 0.013 0.001 TYR B 264 ARG 0.007 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4377.07 seconds wall clock time: 77 minutes 51.42 seconds (4671.42 seconds total)