Starting phenix.real_space_refine on Fri Jul 25 17:34:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cx3_30490/07_2025/7cx3_30490.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cx3_30490/07_2025/7cx3_30490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cx3_30490/07_2025/7cx3_30490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cx3_30490/07_2025/7cx3_30490.map" model { file = "/net/cci-nas-00/data/ceres_data/7cx3_30490/07_2025/7cx3_30490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cx3_30490/07_2025/7cx3_30490.cif" } resolution = 2.8 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= 0.013 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 53 5.16 5 C 5023 2.51 5 N 1373 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7923 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2012 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1870 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} 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: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'GNO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.76, per 1000 atoms: 0.60 Number of scatterers: 7923 At special positions: 0 Unit cell: (76.05, 110.526, 125.736, 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 53 16.00 O 1474 8.00 N 1373 7.00 C 5023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 1.81 Conformation dependent library (CDL) restraints added in 1.0 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 41.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'R' and resid 27 through 45 Processing helix chain 'R' and resid 66 through 95 Proline residue: R 87 - end of helix removed outlier: 4.016A pdb=" N SER R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.724A pdb=" N TYR R 111 " --> pdb=" O ARG R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 148 removed outlier: 3.684A pdb=" N VAL R 148 " --> pdb=" O TYR R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 154 removed outlier: 3.793A pdb=" N LEU R 154 " --> pdb=" O SER R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 170 Processing helix chain 'R' and resid 171 through 174 Processing helix chain 'R' and resid 195 through 229 removed outlier: 3.972A pdb=" N LEU R 199 " --> pdb=" O ALA R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 276 Processing helix chain 'R' and resid 277 through 285 removed outlier: 4.538A pdb=" N THR R 281 " --> pdb=" O SER R 277 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 295 removed outlier: 3.507A pdb=" N SER R 291 " --> pdb=" O ASN R 287 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS R 293 " --> pdb=" O THR R 289 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU R 294 " --> pdb=" O SER R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 317 removed outlier: 3.760A pdb=" N LEU R 301 " --> pdb=" O ASP R 297 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 319 through 330 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.603A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.645A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.493A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.874A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.933A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 392 removed outlier: 3.527A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.647A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 removed outlier: 4.458A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.523A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.518A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.630A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.515A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.750A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.960A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.225A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.597A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.591A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.845A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.243A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1161 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: 2.21 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1460 1.33 - 1.45: 2083 1.45 - 1.57: 4464 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8083 Sorted by residual: bond pdb=" C16 GNO R 401 " pdb=" C9 GNO R 401 " ideal model delta sigma weight residual 1.386 1.527 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C12 GNO R 401 " pdb=" C7 GNO R 401 " ideal model delta sigma weight residual 1.387 1.527 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C4 GNO R 401 " pdb=" C8 GNO R 401 " ideal model delta sigma weight residual 1.386 1.525 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C3 GNO R 401 " pdb=" C6 GNO R 401 " ideal model delta sigma weight residual 1.392 1.527 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C10 GNO R 401 " pdb=" C11 GNO R 401 " ideal model delta sigma weight residual 1.392 1.526 -0.134 2.00e-02 2.50e+03 4.49e+01 ... (remaining 8078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 10922 3.67 - 7.34: 36 7.34 - 11.00: 4 11.00 - 14.67: 0 14.67 - 18.34: 2 Bond angle restraints: 10964 Sorted by residual: angle pdb=" N ALA A 351 " pdb=" CA ALA A 351 " pdb=" C ALA A 351 " ideal model delta sigma weight residual 111.36 126.41 -15.05 1.09e+00 8.42e-01 1.91e+02 angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 111.07 120.76 -9.69 1.07e+00 8.73e-01 8.20e+01 angle pdb=" N THR A 350 " pdb=" CA THR A 350 " pdb=" C THR A 350 " ideal model delta sigma weight residual 111.36 119.57 -8.21 1.09e+00 8.42e-01 5.67e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 111.28 118.75 -7.47 1.09e+00 8.42e-01 4.69e+01 angle pdb=" O1 GNO R 401 " pdb=" S1 GNO R 401 " pdb=" O2 GNO R 401 " ideal model delta sigma weight residual 120.12 101.78 18.34 3.00e+00 1.11e-01 3.74e+01 ... (remaining 10959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4438 17.95 - 35.90: 314 35.90 - 53.85: 48 53.85 - 71.80: 8 71.80 - 89.76: 4 Dihedral angle restraints: 4812 sinusoidal: 1844 harmonic: 2968 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C ALA A 351 " pdb=" N ALA A 351 " pdb=" CA ALA A 351 " pdb=" CB ALA A 351 " ideal model delta harmonic sigma weight residual -122.60 -132.76 10.16 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 4809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1197 0.105 - 0.210: 42 0.210 - 0.315: 7 0.315 - 0.420: 0 0.420 - 0.525: 1 Chirality restraints: 1247 Sorted by residual: chirality pdb=" CA ALA A 351 " pdb=" N ALA A 351 " pdb=" C ALA A 351 " pdb=" CB ALA A 351 " both_signs ideal model delta sigma weight residual False 2.48 1.96 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA TYR A 391 " pdb=" N TYR A 391 " pdb=" C TYR A 391 " pdb=" CB TYR A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1244 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 349 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER A 349 " -0.062 2.00e-02 2.50e+03 pdb=" O SER A 349 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 350 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.017 2.00e-02 2.50e+03 1.56e-02 4.88e+00 pdb=" CG TYR B 59 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 103 2.67 - 3.23: 7229 3.23 - 3.78: 11974 3.78 - 4.34: 17059 4.34 - 4.90: 28418 Nonbonded interactions: 64783 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.109 3.040 nonbonded pdb=" OD1 ASN A 292 " pdb=" OG1 THR A 364 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.242 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.255 3.040 nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.290 3.040 ... (remaining 64778 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: 0.440 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.700 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.006 0.141 8086 Z= 0.290 Angle : 0.665 18.338 10970 Z= 0.407 Chirality : 0.049 0.525 1247 Planarity : 0.004 0.039 1400 Dihedral : 12.663 89.755 2881 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: -1.96 (0.24), residues: 1001 helix: -0.57 (0.23), residues: 383 sheet: -0.63 (0.32), residues: 219 loop : -2.37 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.038 0.002 TYR B 59 ARG 0.002 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.13800 ( 408) hydrogen bonds : angle 5.44596 ( 1161) SS BOND : bond 0.00304 ( 3) SS BOND : angle 1.52281 ( 6) covalent geometry : bond 0.00565 ( 8083) covalent geometry : angle 0.66376 (10964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.901 Fit side-chains REVERT: R 27 ILE cc_start: 0.7262 (mt) cc_final: 0.7023 (tt) REVERT: A 343 ASP cc_start: 0.7603 (m-30) cc_final: 0.7263 (m-30) REVERT: A 386 MET cc_start: 0.7647 (ttm) cc_final: 0.7222 (mtp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 1.3360 time to fit residues: 222.0594 Evaluate side-chains 125 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 0.0670 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 191 HIS A 220 HIS B 17 GLN B 44 GLN N 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123511 restraints weight = 8722.937| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.15 r_work: 0.3280 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8086 Z= 0.105 Angle : 0.509 9.635 10970 Z= 0.268 Chirality : 0.041 0.150 1247 Planarity : 0.004 0.047 1400 Dihedral : 4.604 46.480 1120 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.91 % Allowed : 11.35 % Favored : 86.74 % 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: -0.62 (0.25), residues: 1001 helix: 0.93 (0.26), residues: 390 sheet: -0.19 (0.34), residues: 215 loop : -1.91 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.012 0.001 TYR B 124 ARG 0.005 0.000 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 408) hydrogen bonds : angle 4.23786 ( 1161) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.77181 ( 6) covalent geometry : bond 0.00221 ( 8083) covalent geometry : angle 0.50880 (10964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: R 225 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7789 (ptm) REVERT: A 38 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7725 (mtp-110) REVERT: A 343 ASP cc_start: 0.8288 (m-30) cc_final: 0.7875 (m-30) REVERT: A 346 LEU cc_start: 0.8536 (mt) cc_final: 0.8292 (mp) REVERT: A 386 MET cc_start: 0.8619 (ttm) cc_final: 0.8211 (mtp) REVERT: B 322 ASP cc_start: 0.8409 (t0) cc_final: 0.7929 (m-30) REVERT: G 14 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7295 (tttp) REVERT: N 105 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7255 (ptt180) outliers start: 16 outliers final: 5 residues processed: 143 average time/residue: 1.3392 time to fit residues: 202.1560 Evaluate side-chains 132 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 111 TYR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 390 GLN B 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119996 restraints weight = 8787.444| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.11 r_work: 0.3211 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8086 Z= 0.153 Angle : 0.550 8.859 10970 Z= 0.287 Chirality : 0.043 0.158 1247 Planarity : 0.004 0.050 1400 Dihedral : 4.577 38.063 1120 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.63 % Allowed : 13.62 % Favored : 83.75 % 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: -0.13 (0.26), residues: 1001 helix: 1.36 (0.26), residues: 391 sheet: 0.03 (0.34), residues: 224 loop : -1.70 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.009 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.013 0.001 TYR B 124 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 408) hydrogen bonds : angle 4.23598 ( 1161) SS BOND : bond 0.00459 ( 3) SS BOND : angle 0.84485 ( 6) covalent geometry : bond 0.00357 ( 8083) covalent geometry : angle 0.54986 (10964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 225 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7885 (ptm) REVERT: A 343 ASP cc_start: 0.8288 (m-30) cc_final: 0.7883 (m-30) REVERT: A 386 MET cc_start: 0.8668 (ttm) cc_final: 0.8237 (mtp) REVERT: B 9 GLN cc_start: 0.6722 (mm110) cc_final: 0.6456 (mm110) REVERT: G 14 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7327 (tttp) REVERT: N 105 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7267 (ptt180) outliers start: 22 outliers final: 14 residues processed: 134 average time/residue: 1.4692 time to fit residues: 206.6600 Evaluate side-chains 134 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 17 GLN B 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.175765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121013 restraints weight = 8740.726| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.13 r_work: 0.3232 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8086 Z= 0.138 Angle : 0.531 9.635 10970 Z= 0.277 Chirality : 0.042 0.196 1247 Planarity : 0.004 0.049 1400 Dihedral : 4.422 37.424 1120 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.99 % Allowed : 14.58 % Favored : 82.44 % 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: 0.10 (0.26), residues: 1001 helix: 1.57 (0.26), residues: 397 sheet: 0.01 (0.34), residues: 226 loop : -1.54 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR B 124 ARG 0.008 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 408) hydrogen bonds : angle 4.14480 ( 1161) SS BOND : bond 0.00414 ( 3) SS BOND : angle 0.70441 ( 6) covalent geometry : bond 0.00321 ( 8083) covalent geometry : angle 0.53101 (10964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.6206 (mm-30) cc_final: 0.6005 (mm-30) REVERT: A 343 ASP cc_start: 0.8273 (m-30) cc_final: 0.7840 (m-30) REVERT: A 378 ASP cc_start: 0.8318 (m-30) cc_final: 0.8108 (m-30) REVERT: A 386 MET cc_start: 0.8644 (ttm) cc_final: 0.8191 (mtp) REVERT: B 9 GLN cc_start: 0.6790 (mm110) cc_final: 0.6494 (mm110) REVERT: B 59 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8010 (t80) REVERT: B 217 MET cc_start: 0.8630 (pmt) cc_final: 0.8355 (pmm) REVERT: G 14 LYS cc_start: 0.8246 (ttpt) cc_final: 0.7306 (tttp) REVERT: N 105 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7203 (ptt180) outliers start: 25 outliers final: 15 residues processed: 138 average time/residue: 1.3658 time to fit residues: 198.5298 Evaluate side-chains 136 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 17 GLN B 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.172620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117439 restraints weight = 8801.804| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.14 r_work: 0.3185 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8086 Z= 0.229 Angle : 0.614 9.675 10970 Z= 0.319 Chirality : 0.045 0.160 1247 Planarity : 0.005 0.051 1400 Dihedral : 4.701 37.343 1120 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.23 % Allowed : 15.41 % Favored : 81.36 % 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: 0.04 (0.26), residues: 1001 helix: 1.45 (0.26), residues: 399 sheet: -0.02 (0.34), residues: 225 loop : -1.50 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.010 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.014 0.002 TYR A 339 ARG 0.007 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 408) hydrogen bonds : angle 4.31167 ( 1161) SS BOND : bond 0.00643 ( 3) SS BOND : angle 0.90826 ( 6) covalent geometry : bond 0.00550 ( 8083) covalent geometry : angle 0.61354 (10964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 190 ARG cc_start: 0.7858 (ttp-110) cc_final: 0.6598 (ptp-170) REVERT: A 343 ASP cc_start: 0.8321 (m-30) cc_final: 0.7874 (m-30) REVERT: B 9 GLN cc_start: 0.6716 (mm110) cc_final: 0.6425 (mm110) REVERT: B 59 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8073 (t80) REVERT: B 217 MET cc_start: 0.8657 (pmt) cc_final: 0.8376 (pmm) REVERT: N 105 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7047 (ptt180) outliers start: 27 outliers final: 20 residues processed: 132 average time/residue: 1.3291 time to fit residues: 184.8115 Evaluate side-chains 135 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 0.0770 chunk 72 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 17 GLN B 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120381 restraints weight = 8715.066| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.13 r_work: 0.3222 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8086 Z= 0.130 Angle : 0.536 9.953 10970 Z= 0.277 Chirality : 0.042 0.193 1247 Planarity : 0.004 0.049 1400 Dihedral : 4.441 37.796 1120 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.99 % Allowed : 16.37 % Favored : 80.65 % 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: 0.30 (0.26), residues: 1001 helix: 1.72 (0.26), residues: 397 sheet: 0.10 (0.34), residues: 224 loop : -1.40 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR B 124 ARG 0.005 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 408) hydrogen bonds : angle 4.13417 ( 1161) SS BOND : bond 0.00414 ( 3) SS BOND : angle 0.66867 ( 6) covalent geometry : bond 0.00299 ( 8083) covalent geometry : angle 0.53593 (10964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 190 ARG cc_start: 0.7832 (ttp-110) cc_final: 0.6749 (ptp-110) REVERT: A 343 ASP cc_start: 0.8313 (m-30) cc_final: 0.7884 (m-30) REVERT: A 378 ASP cc_start: 0.8293 (m-30) cc_final: 0.8065 (m-30) REVERT: A 386 MET cc_start: 0.8637 (ttm) cc_final: 0.8180 (mtp) REVERT: B 9 GLN cc_start: 0.6746 (mm110) cc_final: 0.6430 (mm110) REVERT: B 59 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8018 (t80) REVERT: B 217 MET cc_start: 0.8647 (pmt) cc_final: 0.8343 (pmm) REVERT: N 105 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7169 (ptt180) outliers start: 25 outliers final: 16 residues processed: 135 average time/residue: 1.3694 time to fit residues: 194.6330 Evaluate side-chains 131 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 17 GLN B 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120106 restraints weight = 8753.408| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.13 r_work: 0.3218 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8086 Z= 0.135 Angle : 0.552 9.562 10970 Z= 0.280 Chirality : 0.043 0.172 1247 Planarity : 0.004 0.049 1400 Dihedral : 4.365 38.135 1120 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.11 % Allowed : 17.56 % Favored : 79.33 % 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: 0.43 (0.26), residues: 1001 helix: 1.81 (0.26), residues: 397 sheet: 0.14 (0.34), residues: 224 loop : -1.29 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR N 95 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 408) hydrogen bonds : angle 4.08291 ( 1161) SS BOND : bond 0.00426 ( 3) SS BOND : angle 0.65741 ( 6) covalent geometry : bond 0.00312 ( 8083) covalent geometry : angle 0.55157 (10964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 190 ARG cc_start: 0.7889 (ttp-110) cc_final: 0.6702 (ptp-170) REVERT: A 38 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7711 (mtm-85) REVERT: A 343 ASP cc_start: 0.8287 (m-30) cc_final: 0.7836 (m-30) REVERT: A 378 ASP cc_start: 0.8268 (m-30) cc_final: 0.8039 (m-30) REVERT: A 386 MET cc_start: 0.8635 (ttm) cc_final: 0.8202 (mtp) REVERT: A 390 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7557 (pt0) REVERT: B 9 GLN cc_start: 0.6718 (mm110) cc_final: 0.6446 (mm110) REVERT: B 59 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8031 (t80) REVERT: N 105 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7221 (ptt180) outliers start: 26 outliers final: 19 residues processed: 128 average time/residue: 1.3855 time to fit residues: 187.0042 Evaluate side-chains 134 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119881 restraints weight = 8780.138| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.14 r_work: 0.3216 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8086 Z= 0.144 Angle : 0.558 11.068 10970 Z= 0.284 Chirality : 0.043 0.152 1247 Planarity : 0.004 0.049 1400 Dihedral : 4.380 40.170 1120 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.46 % Allowed : 17.56 % Favored : 78.97 % 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: 0.46 (0.26), residues: 1001 helix: 1.85 (0.26), residues: 396 sheet: 0.08 (0.34), residues: 226 loop : -1.23 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR N 95 ARG 0.006 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 408) hydrogen bonds : angle 4.10821 ( 1161) SS BOND : bond 0.00457 ( 3) SS BOND : angle 0.66081 ( 6) covalent geometry : bond 0.00338 ( 8083) covalent geometry : angle 0.55776 (10964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8186 (tt0) cc_final: 0.7898 (tt0) REVERT: A 38 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7692 (mtm-85) REVERT: A 343 ASP cc_start: 0.8267 (m-30) cc_final: 0.7804 (m-30) REVERT: A 378 ASP cc_start: 0.8253 (m-30) cc_final: 0.8033 (m-30) REVERT: A 386 MET cc_start: 0.8638 (ttm) cc_final: 0.8209 (mtp) REVERT: A 390 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7544 (pt0) REVERT: B 9 GLN cc_start: 0.6822 (mm110) cc_final: 0.6531 (mm110) REVERT: B 59 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8023 (t80) REVERT: B 217 MET cc_start: 0.8736 (pmt) cc_final: 0.8411 (pmm) REVERT: N 105 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7209 (ptt180) outliers start: 29 outliers final: 20 residues processed: 130 average time/residue: 1.3593 time to fit residues: 186.0349 Evaluate side-chains 133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.177102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122043 restraints weight = 8900.037| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.15 r_work: 0.3249 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8086 Z= 0.108 Angle : 0.542 11.377 10970 Z= 0.272 Chirality : 0.042 0.203 1247 Planarity : 0.004 0.048 1400 Dihedral : 4.230 41.991 1120 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.87 % Allowed : 18.40 % Favored : 78.73 % 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: 1001 helix: 1.97 (0.26), residues: 396 sheet: 0.15 (0.34), residues: 224 loop : -1.19 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.011 0.001 TYR N 95 ARG 0.005 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 408) hydrogen bonds : angle 4.01131 ( 1161) SS BOND : bond 0.00346 ( 3) SS BOND : angle 0.57231 ( 6) covalent geometry : bond 0.00242 ( 8083) covalent geometry : angle 0.54239 (10964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7625 (mtm-85) REVERT: A 343 ASP cc_start: 0.8273 (m-30) cc_final: 0.7815 (m-30) REVERT: A 378 ASP cc_start: 0.8265 (m-30) cc_final: 0.8039 (m-30) REVERT: A 386 MET cc_start: 0.8667 (ttm) cc_final: 0.8205 (mtp) REVERT: A 390 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7599 (pt0) REVERT: G 14 LYS cc_start: 0.8258 (ttpt) cc_final: 0.7317 (tttp) REVERT: N 105 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7220 (ptt180) outliers start: 24 outliers final: 16 residues processed: 131 average time/residue: 1.4546 time to fit residues: 200.5582 Evaluate side-chains 134 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 26 optimal weight: 0.9980 chunk 91 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.176544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121498 restraints weight = 8680.610| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.13 r_work: 0.3239 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8086 Z= 0.122 Angle : 0.554 11.683 10970 Z= 0.279 Chirality : 0.042 0.185 1247 Planarity : 0.004 0.048 1400 Dihedral : 4.247 41.635 1120 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.75 % Allowed : 18.64 % Favored : 78.61 % 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: 0.61 (0.27), residues: 1001 helix: 1.96 (0.26), residues: 397 sheet: 0.14 (0.35), residues: 224 loop : -1.12 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR B 124 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 408) hydrogen bonds : angle 4.02296 ( 1161) SS BOND : bond 0.00383 ( 3) SS BOND : angle 0.60379 ( 6) covalent geometry : bond 0.00278 ( 8083) covalent geometry : angle 0.55393 (10964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 190 ARG cc_start: 0.8012 (ttp-110) cc_final: 0.6894 (ptp-110) REVERT: A 38 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7684 (mtm-85) REVERT: A 343 ASP cc_start: 0.8281 (m-30) cc_final: 0.7827 (m-30) REVERT: A 378 ASP cc_start: 0.8237 (m-30) cc_final: 0.8019 (m-30) REVERT: A 386 MET cc_start: 0.8674 (ttm) cc_final: 0.8214 (mtp) REVERT: A 390 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7622 (pt0) REVERT: B 217 MET cc_start: 0.8746 (pmt) cc_final: 0.8415 (pmm) REVERT: G 14 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7328 (tttp) REVERT: N 105 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7212 (ptt180) outliers start: 23 outliers final: 18 residues processed: 128 average time/residue: 1.4506 time to fit residues: 195.2603 Evaluate side-chains 133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 MET Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.174757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119700 restraints weight = 8814.624| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.14 r_work: 0.3207 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8086 Z= 0.158 Angle : 0.584 11.683 10970 Z= 0.295 Chirality : 0.043 0.176 1247 Planarity : 0.004 0.048 1400 Dihedral : 4.377 39.152 1120 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.39 % Allowed : 19.00 % Favored : 78.61 % 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: 0.52 (0.26), residues: 1001 helix: 1.85 (0.26), residues: 397 sheet: 0.11 (0.34), residues: 227 loop : -1.15 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.014 0.001 TYR N 95 ARG 0.006 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 408) hydrogen bonds : angle 4.10061 ( 1161) SS BOND : bond 0.00489 ( 3) SS BOND : angle 0.70914 ( 6) covalent geometry : bond 0.00373 ( 8083) covalent geometry : angle 0.58409 (10964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7281.69 seconds wall clock time: 124 minutes 19.96 seconds (7459.96 seconds total)