Starting phenix.real_space_refine on Wed Mar 12 13:08:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cx4_30491/03_2025/7cx4_30491.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cx4_30491/03_2025/7cx4_30491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cx4_30491/03_2025/7cx4_30491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cx4_30491/03_2025/7cx4_30491.map" model { file = "/net/cci-nas-00/data/ceres_data/7cx4_30491/03_2025/7cx4_30491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cx4_30491/03_2025/7cx4_30491.cif" } resolution = 2.9 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= 0.011 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 5026 2.51 5 N 1372 2.21 5 O 1475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 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: 7926 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2016 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 11, 'TRANS': 254} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GM9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.69, per 1000 atoms: 0.59 Number of scatterers: 7926 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 1475 8.00 N 1372 7.00 C 5026 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=2.04 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: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 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: 29 helices and 11 sheets defined 40.5% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'R' and resid 25 through 45 removed outlier: 3.512A pdb=" N MET R 31 " --> pdb=" O ILE R 27 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 92 Proline residue: R 87 - end of helix removed outlier: 3.685A pdb=" N SER R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.573A pdb=" N TYR R 111 " --> pdb=" O ARG R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 148 removed outlier: 3.590A pdb=" N ARG R 146 " --> pdb=" O TYR R 142 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG R 147 " --> pdb=" O PHE R 143 " (cutoff:3.500A) removed outlier: 3.647A 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 228 removed outlier: 3.797A 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 284 removed outlier: 3.847A pdb=" N THR R 281 " --> pdb=" O SER R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 295 Processing helix chain 'R' and resid 296 through 317 removed outlier: 3.546A pdb=" N LEU R 301 " --> pdb=" O ASP R 297 " (cutoff:3.500A) removed outlier: 3.795A 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: 3.660A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.863A 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 235 through 239 removed outlier: 3.626A 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 293 through 304 removed outlier: 3.869A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.920A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 389 through 392 removed outlier: 3.512A pdb=" N GLU A 392 " --> pdb=" O ARG A 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 389 through 392' Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.687A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.662A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.039A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.603A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.562A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.725A 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: 4.830A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.528A 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: 3.509A 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: 6.766A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.901A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.461A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.352A 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: 3.568A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.608A 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: 6.723A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.579A 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: 3.728A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.373A 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: 6.850A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1140 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: 2.30 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2594 1.34 - 1.47: 1990 1.47 - 1.59: 3425 1.59 - 1.72: 0 1.72 - 1.84: 76 Bond restraints: 8085 Sorted by residual: bond pdb=" C25 GM9 R 401 " pdb=" O04 GM9 R 401 " ideal model delta sigma weight residual 1.246 1.355 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" N01 GM9 R 401 " pdb=" S01 GM9 R 401 " ideal model delta sigma weight residual 1.640 1.723 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C24 GM9 R 401 " pdb=" C25 GM9 R 401 " ideal model delta sigma weight residual 1.541 1.505 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" C ARG R 147 " pdb=" O ARG R 147 " ideal model delta sigma weight residual 1.237 1.218 0.019 1.17e-02 7.31e+03 2.51e+00 bond pdb=" C LEU R 157 " pdb=" O LEU R 157 " ideal model delta sigma weight residual 1.244 1.231 0.013 9.80e-03 1.04e+04 1.75e+00 ... (remaining 8080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 10744 1.82 - 3.65: 186 3.65 - 5.47: 31 5.47 - 7.29: 4 7.29 - 9.12: 3 Bond angle restraints: 10968 Sorted by residual: angle pdb=" N ARG R 147 " pdb=" CA ARG R 147 " pdb=" C ARG R 147 " ideal model delta sigma weight residual 111.28 119.77 -8.49 1.09e+00 8.42e-01 6.07e+01 angle pdb=" C GLY A 355 " pdb=" N ARG A 356 " pdb=" CA ARG A 356 " ideal model delta sigma weight residual 122.36 113.24 9.12 1.42e+00 4.96e-01 4.12e+01 angle pdb=" CA LEU R 157 " pdb=" C LEU R 157 " pdb=" N PRO R 158 " ideal model delta sigma weight residual 120.93 117.05 3.88 1.06e+00 8.90e-01 1.34e+01 angle pdb=" C LEU R 157 " pdb=" N PRO R 158 " pdb=" CA PRO R 158 " ideal model delta sigma weight residual 119.05 122.80 -3.75 1.11e+00 8.12e-01 1.14e+01 angle pdb=" N ARG R 146 " pdb=" CA ARG R 146 " pdb=" C ARG R 146 " ideal model delta sigma weight residual 112.68 116.98 -4.30 1.33e+00 5.65e-01 1.04e+01 ... (remaining 10963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4399 17.53 - 35.06: 345 35.06 - 52.59: 52 52.59 - 70.12: 10 70.12 - 87.65: 5 Dihedral angle restraints: 4811 sinusoidal: 1842 harmonic: 2969 Sorted by residual: dihedral pdb=" CB CYS R 109 " pdb=" SG CYS R 109 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual 93.00 5.35 87.65 1 1.00e+01 1.00e-02 9.21e+01 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 -86.00 -9.03 -76.97 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 4808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1163 0.084 - 0.168: 83 0.168 - 0.252: 0 0.252 - 0.336: 0 0.336 - 0.420: 1 Chirality restraints: 1247 Sorted by residual: chirality pdb=" CA ARG R 147 " pdb=" N ARG R 147 " pdb=" C ARG R 147 " pdb=" CB ARG R 147 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+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 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 1244 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 352 " -0.014 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C SER A 352 " 0.051 2.00e-02 2.50e+03 pdb=" O SER A 352 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY A 353 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 318 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C LEU R 318 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU R 318 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG R 319 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.016 2.00e-02 2.50e+03 1.48e-02 4.39e+00 pdb=" CG TYR B 59 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.001 2.00e-02 2.50e+03 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 68 2.61 - 3.18: 6603 3.18 - 3.75: 11938 3.75 - 4.33: 17063 4.33 - 4.90: 28968 Nonbonded interactions: 64640 Sorted by model distance: nonbonded pdb=" O ARG A 283 " pdb=" O GLY A 355 " model vdw 2.032 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.106 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.129 3.040 nonbonded pdb=" OG SER A 251 " pdb=" O LYS A 293 " model vdw 2.130 3.040 nonbonded pdb=" O ALA A 351 " pdb=" OG SER A 352 " model vdw 2.169 3.040 ... (remaining 64635 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: 0.560 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.610 Find NCS groups from input model: 0.080 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 8085 Z= 0.268 Angle : 0.643 9.118 10968 Z= 0.386 Chirality : 0.045 0.420 1247 Planarity : 0.004 0.040 1400 Dihedral : 12.918 81.309 2880 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: -1.78 (0.24), residues: 1002 helix: -0.41 (0.25), residues: 374 sheet: -1.00 (0.30), residues: 232 loop : -1.94 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.010 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.036 0.001 TYR B 59 ARG 0.005 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7986 (tt0) REVERT: B 61 MET cc_start: 0.8513 (tmm) cc_final: 0.8190 (ptm) REVERT: B 246 ASP cc_start: 0.7973 (m-30) cc_final: 0.7598 (m-30) REVERT: N 3 GLN cc_start: 0.7641 (tp40) cc_final: 0.7041 (mt0) REVERT: N 38 ARG cc_start: 0.8908 (ptt180) cc_final: 0.8636 (ptp90) outliers start: 0 outliers final: 1 residues processed: 179 average time/residue: 1.2422 time to fit residues: 234.7359 Evaluate side-chains 138 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 35 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 16 ASN B 268 ASN N 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.165664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125423 restraints weight = 9360.609| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.37 r_work: 0.3275 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8085 Z= 0.233 Angle : 0.585 9.539 10968 Z= 0.303 Chirality : 0.043 0.159 1247 Planarity : 0.004 0.046 1400 Dihedral : 4.852 38.339 1121 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.75 % Allowed : 12.07 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 1002 helix: 0.83 (0.27), residues: 382 sheet: -0.60 (0.32), residues: 231 loop : -1.44 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.009 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.006 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 31 MET cc_start: 0.7882 (ttm) cc_final: 0.7675 (ttp) REVERT: R 166 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7943 (tm) REVERT: A 32 LYS cc_start: 0.7594 (mtpp) cc_final: 0.7264 (mtmm) REVERT: A 35 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7017 (tt0) REVERT: A 314 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8022 (tt0) REVERT: A 378 ASP cc_start: 0.8265 (m-30) cc_final: 0.7965 (m-30) REVERT: B 61 MET cc_start: 0.9017 (tmm) cc_final: 0.8520 (ptm) REVERT: B 155 ASN cc_start: 0.8256 (t0) cc_final: 0.7737 (t0) REVERT: B 219 ARG cc_start: 0.8350 (mmt-90) cc_final: 0.8137 (mtt-85) REVERT: B 254 ASP cc_start: 0.8586 (t0) cc_final: 0.8197 (t0) REVERT: G 36 ASP cc_start: 0.8267 (m-30) cc_final: 0.8023 (m-30) outliers start: 23 outliers final: 7 residues processed: 145 average time/residue: 1.1386 time to fit residues: 175.6517 Evaluate side-chains 135 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126110 restraints weight = 9514.647| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.24 r_work: 0.3282 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8085 Z= 0.199 Angle : 0.541 8.746 10968 Z= 0.280 Chirality : 0.042 0.218 1247 Planarity : 0.004 0.052 1400 Dihedral : 4.463 33.066 1119 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.87 % Allowed : 13.74 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1002 helix: 1.34 (0.27), residues: 384 sheet: -0.43 (0.32), residues: 224 loop : -1.22 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.015 0.001 TYR N 60 ARG 0.006 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 166 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7913 (tm) REVERT: A 314 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8016 (tt0) REVERT: A 378 ASP cc_start: 0.8194 (m-30) cc_final: 0.7920 (m-30) REVERT: B 137 ARG cc_start: 0.8376 (mmt-90) cc_final: 0.7694 (tpp80) REVERT: B 155 ASN cc_start: 0.8260 (t0) cc_final: 0.7740 (t0) REVERT: B 197 ARG cc_start: 0.7605 (mmm-85) cc_final: 0.6630 (mmm-85) REVERT: B 254 ASP cc_start: 0.8612 (t0) cc_final: 0.8120 (t0) REVERT: G 36 ASP cc_start: 0.8164 (m-30) cc_final: 0.7918 (m-30) REVERT: G 47 GLU cc_start: 0.8252 (mp0) cc_final: 0.8046 (mp0) outliers start: 24 outliers final: 10 residues processed: 152 average time/residue: 1.2233 time to fit residues: 196.8793 Evaluate side-chains 139 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 270 ILE 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 15 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127122 restraints weight = 9417.983| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.24 r_work: 0.3292 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8085 Z= 0.178 Angle : 0.531 8.647 10968 Z= 0.274 Chirality : 0.042 0.199 1247 Planarity : 0.004 0.054 1400 Dihedral : 4.382 34.578 1119 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.27 % Allowed : 15.29 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.26 (0.27), residues: 1002 helix: 1.63 (0.27), residues: 384 sheet: -0.18 (0.32), residues: 222 loop : -1.04 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.017 0.001 TYR N 60 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 166 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7856 (tm) REVERT: A 38 ARG cc_start: 0.8240 (mpt180) cc_final: 0.7865 (ttp-170) REVERT: A 314 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7978 (tt0) REVERT: A 378 ASP cc_start: 0.8165 (m-30) cc_final: 0.7906 (m-30) REVERT: B 137 ARG cc_start: 0.8462 (mmt-90) cc_final: 0.7726 (tpp80) REVERT: B 155 ASN cc_start: 0.8257 (t0) cc_final: 0.7743 (t0) REVERT: B 197 ARG cc_start: 0.7533 (mmm-85) cc_final: 0.6837 (mmm-85) REVERT: B 212 ASP cc_start: 0.8124 (t0) cc_final: 0.7743 (t70) REVERT: B 214 ARG cc_start: 0.7933 (mpt180) cc_final: 0.7533 (mpt180) REVERT: B 254 ASP cc_start: 0.8621 (t0) cc_final: 0.8135 (t0) REVERT: G 47 GLU cc_start: 0.8245 (mp0) cc_final: 0.7991 (mp0) REVERT: N 78 THR cc_start: 0.8833 (m) cc_final: 0.8540 (t) outliers start: 19 outliers final: 10 residues processed: 147 average time/residue: 1.2079 time to fit residues: 188.2126 Evaluate side-chains 138 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 270 ILE 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 23 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 17 GLN B 268 ASN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.169669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127652 restraints weight = 9454.591| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.33 r_work: 0.3309 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8085 Z= 0.179 Angle : 0.524 8.425 10968 Z= 0.270 Chirality : 0.041 0.168 1247 Planarity : 0.004 0.055 1400 Dihedral : 4.314 32.802 1119 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.87 % Allowed : 15.53 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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 (0.27), residues: 1002 helix: 1.77 (0.27), residues: 383 sheet: -0.05 (0.33), residues: 222 loop : -0.92 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.019 0.001 TYR N 60 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 166 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7815 (tm) REVERT: A 38 ARG cc_start: 0.8315 (mpt180) cc_final: 0.7943 (ttp-170) REVERT: A 53 LYS cc_start: 0.6574 (ptmt) cc_final: 0.6211 (ttpt) REVERT: A 314 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8009 (tt0) REVERT: B 137 ARG cc_start: 0.8535 (mmt-90) cc_final: 0.7962 (tpp80) REVERT: B 155 ASN cc_start: 0.8327 (t0) cc_final: 0.7843 (t0) REVERT: B 197 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.6858 (mmm-85) REVERT: B 214 ARG cc_start: 0.7960 (mpt180) cc_final: 0.7660 (mpt180) REVERT: B 254 ASP cc_start: 0.8562 (t0) cc_final: 0.8231 (t0) outliers start: 24 outliers final: 12 residues processed: 143 average time/residue: 1.2834 time to fit residues: 194.2084 Evaluate side-chains 141 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 270 ILE 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 69 optimal weight: 0.0020 chunk 74 optimal weight: 0.0670 chunk 82 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.172179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130778 restraints weight = 9402.874| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.30 r_work: 0.3327 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8085 Z= 0.139 Angle : 0.501 8.610 10968 Z= 0.257 Chirality : 0.040 0.146 1247 Planarity : 0.004 0.055 1400 Dihedral : 4.119 29.976 1119 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.63 % Allowed : 17.20 % Favored : 80.17 % 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: 0.68 (0.27), residues: 1002 helix: 1.95 (0.27), residues: 382 sheet: 0.09 (0.33), residues: 221 loop : -0.80 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.019 0.001 TYR N 60 ARG 0.006 0.000 ARG R 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 166 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7807 (tm) REVERT: A 35 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7154 (tt0) REVERT: A 38 ARG cc_start: 0.8249 (mpt180) cc_final: 0.7903 (ttp-170) REVERT: A 53 LYS cc_start: 0.6541 (ptmt) cc_final: 0.6194 (ttpt) REVERT: A 314 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8057 (tt0) REVERT: B 137 ARG cc_start: 0.8562 (mmt-90) cc_final: 0.8302 (tpp-160) REVERT: B 155 ASN cc_start: 0.8237 (t0) cc_final: 0.7745 (t0) REVERT: B 197 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.6919 (mmm-85) REVERT: B 212 ASP cc_start: 0.8027 (t0) cc_final: 0.7703 (t70) REVERT: B 214 ARG cc_start: 0.7963 (mpt180) cc_final: 0.7638 (mpt180) REVERT: B 254 ASP cc_start: 0.8450 (t0) cc_final: 0.8181 (t0) outliers start: 22 outliers final: 11 residues processed: 148 average time/residue: 1.1917 time to fit residues: 186.7319 Evaluate side-chains 138 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 111 TYR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 268 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128045 restraints weight = 9583.304| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.32 r_work: 0.3299 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8085 Z= 0.228 Angle : 0.561 8.792 10968 Z= 0.287 Chirality : 0.042 0.156 1247 Planarity : 0.004 0.055 1400 Dihedral : 4.379 36.575 1119 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.63 % Allowed : 17.92 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 1002 helix: 1.87 (0.27), residues: 382 sheet: 0.05 (0.33), residues: 222 loop : -0.82 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.021 0.001 TYR N 60 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 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: 22 poor density : 125 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 107 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6251 (ptp-170) REVERT: R 166 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7721 (tm) REVERT: R 191 HIS cc_start: 0.8945 (m90) cc_final: 0.8479 (m-70) REVERT: A 38 ARG cc_start: 0.8333 (mpt180) cc_final: 0.7902 (ttp-170) REVERT: A 53 LYS cc_start: 0.6554 (ptmt) cc_final: 0.6258 (ttpt) REVERT: A 314 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8068 (tt0) REVERT: A 356 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7166 (mmp-170) REVERT: B 137 ARG cc_start: 0.8481 (mmt-90) cc_final: 0.7906 (tpp80) REVERT: B 155 ASN cc_start: 0.8331 (t0) cc_final: 0.7839 (t0) REVERT: B 197 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.6792 (mmm-85) REVERT: B 214 ARG cc_start: 0.7976 (mpt180) cc_final: 0.7622 (mpt180) REVERT: B 254 ASP cc_start: 0.8564 (t0) cc_final: 0.8226 (t0) outliers start: 22 outliers final: 12 residues processed: 137 average time/residue: 1.3076 time to fit residues: 189.0069 Evaluate side-chains 135 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 MET Chi-restraints excluded: chain R residue 107 ARG Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS 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 0 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.170663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128789 restraints weight = 9498.862| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.31 r_work: 0.3303 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8085 Z= 0.179 Angle : 0.527 8.959 10968 Z= 0.270 Chirality : 0.041 0.145 1247 Planarity : 0.004 0.055 1400 Dihedral : 4.288 35.304 1119 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.03 % Allowed : 19.12 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.65 (0.27), residues: 1002 helix: 1.90 (0.27), residues: 382 sheet: 0.10 (0.33), residues: 222 loop : -0.79 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.019 0.001 TYR N 60 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 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: 17 poor density : 123 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 107 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6277 (ptp-170) REVERT: R 166 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7753 (tm) REVERT: R 190 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8422 (ttp-110) REVERT: R 191 HIS cc_start: 0.8875 (m90) cc_final: 0.8419 (m-70) REVERT: A 38 ARG cc_start: 0.8330 (mpt180) cc_final: 0.7932 (ttp-170) REVERT: A 53 LYS cc_start: 0.6541 (ptmt) cc_final: 0.6257 (ttpt) REVERT: A 314 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8097 (tt0) REVERT: A 356 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7076 (mmp-170) REVERT: B 137 ARG cc_start: 0.8522 (mmt-90) cc_final: 0.7889 (tpp80) REVERT: B 155 ASN cc_start: 0.8290 (t0) cc_final: 0.7854 (t0) REVERT: B 197 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.6933 (mmm-85) REVERT: B 212 ASP cc_start: 0.8113 (t0) cc_final: 0.7811 (t70) REVERT: B 214 ARG cc_start: 0.7973 (mpt180) cc_final: 0.7616 (mpt180) REVERT: B 217 MET cc_start: 0.7905 (ptt) cc_final: 0.7629 (pp-130) REVERT: B 254 ASP cc_start: 0.8457 (t0) cc_final: 0.8247 (t0) outliers start: 17 outliers final: 10 residues processed: 133 average time/residue: 1.2664 time to fit residues: 177.8549 Evaluate side-chains 130 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 ARG Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 0.0050 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 17 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.167959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127038 restraints weight = 9698.528| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.39 r_work: 0.3293 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8085 Z= 0.255 Angle : 0.571 8.769 10968 Z= 0.293 Chirality : 0.043 0.157 1247 Planarity : 0.004 0.056 1400 Dihedral : 4.480 37.580 1119 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.51 % Allowed : 18.64 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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 (0.27), residues: 1002 helix: 1.84 (0.27), residues: 382 sheet: 0.08 (0.33), residues: 228 loop : -0.79 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.022 0.001 TYR N 60 ARG 0.007 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 107 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6230 (ptp-170) REVERT: R 166 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7764 (tm) REVERT: R 191 HIS cc_start: 0.8877 (m90) cc_final: 0.8425 (m-70) REVERT: A 53 LYS cc_start: 0.6493 (ptmt) cc_final: 0.6202 (ttpt) REVERT: A 314 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8130 (tt0) REVERT: B 155 ASN cc_start: 0.8342 (t0) cc_final: 0.7860 (t0) REVERT: B 197 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.6797 (mmm-85) REVERT: B 214 ARG cc_start: 0.8027 (mpt180) cc_final: 0.7702 (mpt180) REVERT: B 254 ASP cc_start: 0.8602 (t0) cc_final: 0.8329 (t0) REVERT: N 78 THR cc_start: 0.8849 (m) cc_final: 0.8595 (t) outliers start: 21 outliers final: 14 residues processed: 140 average time/residue: 1.3384 time to fit residues: 197.5851 Evaluate side-chains 143 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 ARG Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS 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 98 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 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 35 GLN B 17 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.170380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128679 restraints weight = 9433.798| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.29 r_work: 0.3321 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8085 Z= 0.179 Angle : 0.534 8.704 10968 Z= 0.275 Chirality : 0.041 0.141 1247 Planarity : 0.004 0.057 1400 Dihedral : 4.314 35.085 1119 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.91 % Allowed : 19.95 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.66 (0.27), residues: 1002 helix: 1.89 (0.27), residues: 382 sheet: 0.15 (0.33), residues: 221 loop : -0.81 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.022 0.001 TYR N 60 ARG 0.008 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 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: 16 poor density : 131 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 107 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6302 (ptp-170) REVERT: R 154 LEU cc_start: 0.7886 (mt) cc_final: 0.7652 (mt) REVERT: R 166 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7702 (tm) REVERT: R 190 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8464 (ttp-110) REVERT: A 38 ARG cc_start: 0.8320 (mpt180) cc_final: 0.7941 (ttp-170) REVERT: A 53 LYS cc_start: 0.6549 (ptmt) cc_final: 0.6278 (ttpt) REVERT: A 314 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8185 (tt0) REVERT: B 137 ARG cc_start: 0.8566 (mmt-90) cc_final: 0.8324 (tpp-160) REVERT: B 155 ASN cc_start: 0.8315 (t0) cc_final: 0.7833 (t0) REVERT: B 197 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.6946 (mmm-85) REVERT: B 212 ASP cc_start: 0.8135 (t0) cc_final: 0.7879 (t70) REVERT: B 214 ARG cc_start: 0.8002 (mpt180) cc_final: 0.7642 (mpt180) REVERT: B 217 MET cc_start: 0.7960 (ptt) cc_final: 0.7677 (pp-130) REVERT: B 254 ASP cc_start: 0.8530 (t0) cc_final: 0.8316 (t0) REVERT: N 78 THR cc_start: 0.8886 (m) cc_final: 0.8642 (t) outliers start: 16 outliers final: 12 residues processed: 139 average time/residue: 1.2997 time to fit residues: 190.6776 Evaluate side-chains 139 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 MET Chi-restraints excluded: chain R residue 107 ARG Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS 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 8 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 17 GLN B 268 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.170275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128363 restraints weight = 9479.929| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.31 r_work: 0.3310 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8085 Z= 0.194 Angle : 0.546 8.606 10968 Z= 0.281 Chirality : 0.042 0.144 1247 Planarity : 0.004 0.057 1400 Dihedral : 4.295 34.801 1119 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.15 % Allowed : 19.83 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.66 (0.27), residues: 1002 helix: 1.87 (0.27), residues: 382 sheet: 0.11 (0.33), residues: 222 loop : -0.76 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.021 0.001 TYR N 60 ARG 0.008 0.000 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6478.45 seconds wall clock time: 110 minutes 50.92 seconds (6650.92 seconds total)