Starting phenix.real_space_refine on Fri Sep 11 05:19:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cx4_30491/09_2026/7cx4_30491.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cx4_30491/09_2026/7cx4_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 { model { file = "/net/cci-nas-00/data/ceres_data/7cx4_30491/09_2026/7cx4_30491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cx4_30491/09_2026/7cx4_30491.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cx4_30491/09_2026/7cx4_30491.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cx4_30491/09_2026/7cx4_30491.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cx4_30491/09_2026/7cx4_30491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cx4_30491/09_2026/7cx4_30491.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ARG:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 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, 'ARG:plan': 1, 'GLU:plan': 2} 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: 1.52, per 1000 atoms: 0.19 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: 0.62 Conformation dependent library (CDL) restraints added in 436.1 milliseconds 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: 0.16 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: 1.07 Time building geometry restraints manager: 0.74 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: 8 70.12 - 87.65: 5 Dihedral angle restraints: 4809 sinusoidal: 1840 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 4806 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: 0.490 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 8088 Z= 0.200 Angle : 0.644 9.118 10974 Z= 0.387 Chirality : 0.045 0.420 1247 Planarity : 0.004 0.040 1400 Dihedral : 12.812 81.309 2878 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.49 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.000 ARG G 13 TYR 0.036 0.001 TYR B 59 PHE 0.013 0.001 PHE A 212 TRP 0.014 0.002 TRP A 234 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 ( 8085) covalent geometry : angle 0.64281 / 0.39 (10968) SS BOND : bond 0.00443 / 0.27 ( 3) SS BOND : angle 2.07773 / 1.25 ( 6) hydrogen bonds : bond 0.13379 / 9.43 ( 397) hydrogen bonds : angle 5.78267 / 4.26 ( 1140) *********************** 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 : 0.283 Fit side-chains revert: symmetry clash REVERT: R 190 ARG cc_start: 0.8630 (ttp-170) cc_final: 0.8407 (tmm-80) 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: 0.8115 (ptm) REVERT: B 246 ASP cc_start: 0.7973 (m-30) cc_final: 0.7597 (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: 0.5289 time to fit residues: 99.7920 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 : 0.297 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 97 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.1321 > 50:) chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3914 r_free = 0.3914 target = 0.165690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124101 restraints weight = 9604.761| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.42 r_work: 0.3264 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8088 Z= 0.225 Angle : 0.661 9.911 10974 Z= 0.342 Chirality : 0.046 0.179 1247 Planarity : 0.005 0.045 1400 Dihedral : 4.888 40.349 1119 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.99 % Allowed : 12.66 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.26), residues: 1002 helix: 0.67 (0.26), residues: 382 sheet: -0.64 (0.31), residues: 231 loop : -1.53 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 137 TYR 0.016 0.002 TYR R 144 PHE 0.016 0.002 PHE A 212 TRP 0.018 0.002 TRP A 234 HIS 0.012 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 ( 8085) covalent geometry : angle 0.64874 / 0.34 (10968) SS BOND : bond 0.00533 / 0.33 ( 3) SS BOND : angle 5.53616 / 3.68 ( 6) hydrogen bonds : bond 0.04595 / 3.12 ( 397) hydrogen bonds : angle 4.57853 / 3.31 ( 1140) *********************** 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 162 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: R 31 MET cc_start: 0.7910 (ttm) cc_final: 0.7697 (ttp) REVERT: R 126 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8434 (mmm) REVERT: A 32 LYS cc_start: 0.7728 (mtpp) cc_final: 0.7410 (mtmm) REVERT: A 314 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8065 (tt0) REVERT: A 378 ASP cc_start: 0.8319 (m-30) cc_final: 0.8013 (m-30) REVERT: B 61 MET cc_start: 0.9114 (tmm) cc_final: 0.8602 (ptm) REVERT: B 155 ASN cc_start: 0.8368 (t0) cc_final: 0.7826 (t0) REVERT: B 254 ASP cc_start: 0.8589 (t0) cc_final: 0.8249 (t0) outliers start: 25 outliers final: 8 residues processed: 146 average time/residue: 0.5982 time to fit residues: 92.1997 Evaluate side-chains 137 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 MET 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 318 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 262 MET 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 68 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 220 HIS A 292 ASN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.165012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123921 restraints weight = 9421.917| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.24 r_work: 0.3262 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8088 Z= 0.147 Angle : 0.565 9.357 10974 Z= 0.293 Chirality : 0.043 0.232 1247 Planarity : 0.004 0.051 1400 Dihedral : 4.523 38.086 1117 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.39 % Allowed : 14.46 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.26), residues: 1002 helix: 1.29 (0.27), residues: 384 sheet: -0.47 (0.32), residues: 224 loop : -1.27 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.015 0.001 TYR N 60 PHE 0.014 0.001 PHE A 212 TRP 0.016 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8085) covalent geometry : angle 0.55604 / 0.29 (10968) SS BOND : bond 0.00610 / 0.33 ( 3) SS BOND : angle 4.25067 / 2.82 ( 6) hydrogen bonds : bond 0.03796 / 2.62 ( 397) hydrogen bonds : angle 4.23582 / 3.04 ( 1140) *********************** 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 156 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 31 MET cc_start: 0.7948 (ttm) cc_final: 0.7616 (ttp) REVERT: R 166 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7954 (tm) REVERT: A 314 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8077 (tt0) REVERT: B 61 MET cc_start: 0.9078 (tmm) cc_final: 0.8598 (ptm) REVERT: B 155 ASN cc_start: 0.8337 (t0) cc_final: 0.7831 (t0) REVERT: B 254 ASP cc_start: 0.8593 (t0) cc_final: 0.8131 (t0) REVERT: G 47 GLU cc_start: 0.8354 (mp0) cc_final: 0.8087 (mp0) outliers start: 20 outliers final: 9 residues processed: 144 average time/residue: 0.5917 time to fit residues: 90.2038 Evaluate side-chains 138 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 71 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 292 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125519 restraints weight = 9568.397| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.35 r_work: 0.3265 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8088 Z= 0.136 Angle : 0.554 8.641 10974 Z= 0.285 Chirality : 0.042 0.199 1247 Planarity : 0.004 0.052 1400 Dihedral : 4.383 34.756 1117 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.75 % Allowed : 16.01 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.27), residues: 1002 helix: 1.58 (0.27), residues: 384 sheet: -0.24 (0.33), residues: 222 loop : -1.09 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.017 0.001 TYR N 60 PHE 0.013 0.001 PHE A 212 TRP 0.016 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8085) covalent geometry : angle 0.54707 / 0.28 (10968) SS BOND : bond 0.00595 / 0.34 ( 3) SS BOND : angle 3.89242 / 2.59 ( 6) hydrogen bonds : bond 0.03634 / 2.51 ( 397) hydrogen bonds : angle 4.12300 / 2.96 ( 1140) *********************** 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 158 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 166 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7847 (tm) REVERT: A 38 ARG cc_start: 0.8270 (mpt180) cc_final: 0.7890 (ttp-170) REVERT: A 314 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8053 (tt0) REVERT: B 9 GLN cc_start: 0.8618 (mm110) cc_final: 0.8168 (mm-40) REVERT: B 61 MET cc_start: 0.9087 (tmm) cc_final: 0.8677 (ptm) REVERT: B 137 ARG cc_start: 0.8469 (mmt-90) cc_final: 0.8153 (tpp-160) REVERT: B 155 ASN cc_start: 0.8269 (t0) cc_final: 0.7786 (t0) REVERT: B 254 ASP cc_start: 0.8670 (t0) cc_final: 0.8262 (t0) REVERT: G 47 GLU cc_start: 0.8235 (mp0) cc_final: 0.8014 (mp0) REVERT: N 78 THR cc_start: 0.8849 (m) cc_final: 0.8587 (t) outliers start: 23 outliers final: 12 residues processed: 147 average time/residue: 0.5696 time to fit residues: 88.8755 Evaluate side-chains 138 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 241 VAL 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 G residue 21 MET 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 1 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 292 ASN B 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.170268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129808 restraints weight = 9549.959| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.36 r_work: 0.3302 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8088 Z= 0.108 Angle : 0.523 8.437 10974 Z= 0.269 Chirality : 0.041 0.173 1247 Planarity : 0.004 0.053 1400 Dihedral : 4.186 31.437 1117 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.27 % Allowed : 17.56 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1002 helix: 1.80 (0.27), residues: 383 sheet: -0.07 (0.33), residues: 222 loop : -0.87 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.017 0.001 TYR N 60 PHE 0.011 0.001 PHE A 212 TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8085) covalent geometry : angle 0.51650 / 0.27 (10968) SS BOND : bond 0.00590 / 0.35 ( 3) SS BOND : angle 3.44943 / 2.28 ( 6) hydrogen bonds : bond 0.03251 / 2.26 ( 397) hydrogen bonds : angle 3.98217 / 2.85 ( 1140) *********************** 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 158 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 166 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7764 (tm) REVERT: A 38 ARG cc_start: 0.8277 (mpt180) cc_final: 0.7881 (ttp-170) REVERT: A 292 ASN cc_start: 0.7333 (t0) cc_final: 0.6997 (t0) REVERT: A 314 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8023 (tt0) REVERT: B 61 MET cc_start: 0.9063 (tmm) cc_final: 0.8765 (ptm) REVERT: B 137 ARG cc_start: 0.8488 (mmt-90) cc_final: 0.8233 (tpp-160) REVERT: B 155 ASN cc_start: 0.8278 (t0) cc_final: 0.7805 (t0) REVERT: B 254 ASP cc_start: 0.8534 (t0) cc_final: 0.8172 (t0) REVERT: G 13 ARG cc_start: 0.7779 (mmp80) cc_final: 0.7383 (mmt90) REVERT: G 47 GLU cc_start: 0.8297 (mp0) cc_final: 0.7933 (mp0) outliers start: 19 outliers final: 10 residues processed: 150 average time/residue: 0.5930 time to fit residues: 94.0561 Evaluate side-chains 141 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 356 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 34 optimal weight: 0.0030 chunk 74 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3915 r_free = 0.3915 target = 0.165829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125123 restraints weight = 9470.141| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.36 r_work: 0.3290 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.004 0.031 8088 Z= 0.158 Angle : 0.570 8.586 10974 Z= 0.290 Chirality : 0.043 0.159 1247 Planarity : 0.004 0.055 1400 Dihedral : 4.343 33.121 1117 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 1002 helix: 1.81 (0.27), residues: 383 sheet: -0.00 (0.33), residues: 223 loop : -0.85 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.018 0.001 TYR N 60 PHE 0.014 0.001 PHE A 212 TRP 0.016 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 8085) covalent geometry : angle 0.56267 / 0.29 (10968) SS BOND : bond 0.00496 / 0.28 ( 3) SS BOND : angle 3.90651 / 2.61 ( 6) hydrogen bonds : bond 0.03750 / 2.58 ( 397) hydrogen bonds : angle 4.10269 / 2.94 ( 1140) *********************** 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: 24 poor density : 135 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 166 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7773 (tm) REVERT: R 190 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8255 (ttp-110) REVERT: A 38 ARG cc_start: 0.8326 (mpt180) cc_final: 0.7924 (ttp-170) REVERT: A 314 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8099 (tt0) REVERT: B 61 MET cc_start: 0.9108 (tmm) cc_final: 0.8680 (ptm) REVERT: B 137 ARG cc_start: 0.8510 (mmt-90) cc_final: 0.7887 (tpp80) REVERT: B 155 ASN cc_start: 0.8360 (t0) cc_final: 0.7892 (t0) REVERT: B 254 ASP cc_start: 0.8582 (t0) cc_final: 0.8247 (t0) outliers start: 24 outliers final: 14 residues processed: 149 average time/residue: 0.6044 time to fit residues: 94.9529 Evaluate side-chains 145 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 241 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 112 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain N residue 96 CYS 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 78 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.168050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127340 restraints weight = 9591.573| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.44 r_work: 0.3297 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8088 Z= 0.146 Angle : 0.573 9.268 10974 Z= 0.291 Chirality : 0.042 0.153 1247 Planarity : 0.004 0.055 1400 Dihedral : 4.376 36.931 1117 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.63 % Allowed : 19.12 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 1002 helix: 1.82 (0.27), residues: 383 sheet: -0.01 (0.33), residues: 222 loop : -0.87 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 347 TYR 0.020 0.001 TYR N 60 PHE 0.013 0.001 PHE A 212 TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 8085) covalent geometry : angle 0.56439 / 0.29 (10968) SS BOND : bond 0.00634 / 0.35 ( 3) SS BOND : angle 4.28454 / 2.78 ( 6) hydrogen bonds : bond 0.03647 / 2.52 ( 397) hydrogen bonds : angle 4.10424 / 2.95 ( 1140) *********************** 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 162 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 166 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7792 (tm) REVERT: R 190 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8266 (ttp-110) REVERT: A 38 ARG cc_start: 0.8316 (mpt180) cc_final: 0.7899 (ttp-170) REVERT: A 53 LYS cc_start: 0.6505 (ptmt) cc_final: 0.6129 (ttpt) REVERT: A 314 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8120 (tt0) REVERT: B 9 GLN cc_start: 0.8628 (mm110) cc_final: 0.8197 (mm-40) REVERT: B 61 MET cc_start: 0.9127 (tmm) cc_final: 0.8718 (ptm) REVERT: B 137 ARG cc_start: 0.8467 (mmt-90) cc_final: 0.7849 (tpp80) REVERT: B 155 ASN cc_start: 0.8321 (t0) cc_final: 0.7897 (t0) REVERT: B 254 ASP cc_start: 0.8581 (t0) cc_final: 0.8225 (t0) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 0.6214 time to fit residues: 99.6652 Evaluate side-chains 149 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 241 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 G residue 13 ARG 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 82 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN B 268 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128728 restraints weight = 9620.302| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.36 r_work: 0.3336 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8088 Z= 0.113 Angle : 0.545 8.945 10974 Z= 0.277 Chirality : 0.041 0.142 1247 Planarity : 0.004 0.055 1400 Dihedral : 4.195 33.831 1117 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.63 % Allowed : 19.47 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 1002 helix: 1.92 (0.27), residues: 383 sheet: 0.03 (0.33), residues: 222 loop : -0.79 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 347 TYR 0.021 0.001 TYR N 60 PHE 0.011 0.001 PHE A 212 TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 8085) covalent geometry : angle 0.53892 / 0.27 (10968) SS BOND : bond 0.00491 / 0.27 ( 3) SS BOND : angle 3.54937 / 2.33 ( 6) hydrogen bonds : bond 0.03254 / 2.25 ( 397) hydrogen bonds : angle 3.98798 / 2.85 ( 1140) *********************** 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 160 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 154 LEU cc_start: 0.7905 (mt) cc_final: 0.7681 (mt) REVERT: R 166 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7708 (tm) REVERT: R 190 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8211 (ttp-110) REVERT: A 38 ARG cc_start: 0.8274 (mpt180) cc_final: 0.7887 (ttp-170) REVERT: A 53 LYS cc_start: 0.6544 (ptmt) cc_final: 0.6266 (ttpt) REVERT: A 314 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8100 (tt0) REVERT: B 61 MET cc_start: 0.9104 (tmm) cc_final: 0.8722 (ptm) REVERT: B 137 ARG cc_start: 0.8489 (mmt-90) cc_final: 0.7808 (tpp80) REVERT: B 155 ASN cc_start: 0.8264 (t0) cc_final: 0.7807 (t0) REVERT: B 254 ASP cc_start: 0.8443 (t0) cc_final: 0.8203 (t0) outliers start: 22 outliers final: 15 residues processed: 151 average time/residue: 0.5879 time to fit residues: 93.8970 Evaluate side-chains 152 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 219 ILE 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 B residue 275 SER Chi-restraints excluded: chain G residue 13 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.166976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127488 restraints weight = 9581.381| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.22 r_work: 0.3278 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8088 Z= 0.147 Angle : 0.590 9.138 10974 Z= 0.297 Chirality : 0.042 0.150 1247 Planarity : 0.004 0.056 1400 Dihedral : 4.343 35.155 1117 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.63 % Allowed : 19.83 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.27), residues: 1002 helix: 1.87 (0.27), residues: 383 sheet: 0.04 (0.33), residues: 222 loop : -0.82 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 347 TYR 0.021 0.001 TYR N 60 PHE 0.013 0.001 PHE A 212 TRP 0.015 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8085) covalent geometry : angle 0.58276 / 0.29 (10968) SS BOND : bond 0.00559 / 0.31 ( 3) SS BOND : angle 3.97993 / 2.63 ( 6) hydrogen bonds : bond 0.03582 / 2.46 ( 397) hydrogen bonds : angle 4.08577 / 2.94 ( 1140) *********************** 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 155 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 107 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6213 (ptp-170) REVERT: R 154 LEU cc_start: 0.7913 (mt) cc_final: 0.7687 (mt) REVERT: R 166 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7656 (tm) REVERT: R 180 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: R 190 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8301 (ttp80) REVERT: R 191 HIS cc_start: 0.8946 (m90) cc_final: 0.8482 (m-70) REVERT: A 38 ARG cc_start: 0.8333 (mpt180) cc_final: 0.7894 (ttp-170) REVERT: A 53 LYS cc_start: 0.6407 (ptmt) cc_final: 0.6119 (ttpt) REVERT: A 314 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8131 (tt0) REVERT: B 61 MET cc_start: 0.9133 (tmm) cc_final: 0.8771 (ptm) REVERT: B 137 ARG cc_start: 0.8476 (mmt-90) cc_final: 0.7876 (tpp80) REVERT: B 155 ASN cc_start: 0.8332 (t0) cc_final: 0.7857 (t0) REVERT: B 217 MET cc_start: 0.8141 (ptt) cc_final: 0.7922 (pp-130) REVERT: B 254 ASP cc_start: 0.8585 (t0) cc_final: 0.8289 (t0) outliers start: 22 outliers final: 13 residues processed: 146 average time/residue: 0.6126 time to fit residues: 94.5093 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 : 0.306 ------------------------------------------------------------------------------- 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 180 GLN Chi-restraints excluded: chain R residue 219 ILE 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 B residue 275 SER Chi-restraints excluded: chain G residue 13 ARG 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 51 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 0.0000 chunk 82 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 0.0170 chunk 47 optimal weight: 0.9980 overall best weight: 0.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.171309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131741 restraints weight = 9542.098| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.29 r_work: 0.3346 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8088 Z= 0.100 Angle : 0.544 9.158 10974 Z= 0.273 Chirality : 0.040 0.133 1247 Planarity : 0.004 0.058 1400 Dihedral : 4.060 30.653 1117 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.55 % Allowed : 21.03 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.27), residues: 1002 helix: 2.04 (0.27), residues: 382 sheet: 0.19 (0.34), residues: 221 loop : -0.72 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 347 TYR 0.022 0.001 TYR N 60 PHE 0.010 0.001 PHE A 212 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 8085) covalent geometry : angle 0.53993 / 0.27 (10968) SS BOND : bond 0.00355 / 0.19 ( 3) SS BOND : angle 2.95454 / 1.95 ( 6) hydrogen bonds : bond 0.02938 / 2.03 ( 397) hydrogen bonds : angle 3.89777 / 2.79 ( 1140) ********************** 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 149 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 45 LEU cc_start: 0.7114 (mp) cc_final: 0.6458 (tt) REVERT: R 107 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6236 (ptp-170) REVERT: R 166 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7632 (tm) REVERT: R 190 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8307 (ttp80) REVERT: R 286 MET cc_start: 0.8451 (mmm) cc_final: 0.8044 (mmp) REVERT: A 35 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7065 (tt0) REVERT: A 38 ARG cc_start: 0.8220 (mpt180) cc_final: 0.7836 (ttp-170) REVERT: A 53 LYS cc_start: 0.6477 (ptmt) cc_final: 0.6249 (ttpt) REVERT: A 314 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8167 (tt0) REVERT: A 356 ARG cc_start: 0.7865 (mtm180) cc_final: 0.7203 (ptt180) REVERT: B 61 MET cc_start: 0.9110 (tmm) cc_final: 0.8857 (ptm) REVERT: B 137 ARG cc_start: 0.8512 (mmt-90) cc_final: 0.8238 (tpp-160) REVERT: B 155 ASN cc_start: 0.8191 (t0) cc_final: 0.7757 (t0) REVERT: B 217 MET cc_start: 0.8029 (ptt) cc_final: 0.7804 (pp-130) REVERT: B 254 ASP cc_start: 0.8448 (t0) cc_final: 0.8222 (t0) outliers start: 13 outliers final: 4 residues processed: 144 average time/residue: 0.5802 time to fit residues: 88.6173 Evaluate side-chains 132 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 275 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 98 SER 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 81 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 93 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.170272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130277 restraints weight = 9500.219| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.35 r_work: 0.3340 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8088 Z= 0.113 Angle : 0.572 10.301 10974 Z= 0.286 Chirality : 0.041 0.134 1247 Planarity : 0.005 0.073 1400 Dihedral : 4.111 30.614 1117 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.91 % Allowed : 21.15 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.27), residues: 1002 helix: 1.96 (0.27), residues: 382 sheet: 0.22 (0.34), residues: 221 loop : -0.72 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG G 13 TYR 0.010 0.001 TYR A 37 PHE 0.010 0.001 PHE A 212 TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 8085) covalent geometry : angle 0.56730 / 0.28 (10968) SS BOND : bond 0.00461 / 0.25 ( 3) SS BOND : angle 3.29123 / 2.19 ( 6) hydrogen bonds : bond 0.03145 / 2.17 ( 397) hydrogen bonds : angle 3.92515 / 2.83 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.23 seconds wall clock time: 56 minutes 17.22 seconds (3377.22 seconds total)