Starting phenix.real_space_refine on Sat Dec 28 05:08:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xtq_33452/12_2024/7xtq_33452.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xtq_33452/12_2024/7xtq_33452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xtq_33452/12_2024/7xtq_33452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xtq_33452/12_2024/7xtq_33452.map" model { file = "/net/cci-nas-00/data/ceres_data/7xtq_33452/12_2024/7xtq_33452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xtq_33452/12_2024/7xtq_33452.cif" } resolution = 3.2 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= 0.002 sd= 0.033 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: 5 Type Number sf(0) Gaussians S 46 5.16 5 Cl 2 4.86 5 C 5066 2.51 5 N 1420 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8010 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "C" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1910 Chain: "B" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2612 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2063 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 251} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'H8I': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 380 " occ=0.50 ... (20 atoms not shown) pdb=" NH2CARG A 380 " occ=0.62 Time building chain proxies: 5.00, per 1000 atoms: 0.62 Number of scatterers: 8010 At special positions: 0 Unit cell: (77.064, 114.582, 122.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 46 16.00 O 1476 8.00 N 1420 7.00 C 5066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 155 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.4 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 40.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.409A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.269A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.732A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.631A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 42 removed outlier: 3.980A pdb=" N ASP R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 67 Processing helix chain 'R' and resid 68 through 75 Proline residue: R 72 - end of helix removed outlier: 4.452A pdb=" N TRP R 75 " --> pdb=" O PRO R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 116 Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 123 through 141 removed outlier: 3.754A pdb=" N ALA R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Proline residue: R 135 - end of helix Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 174 removed outlier: 3.975A pdb=" N LEU R 174 " --> pdb=" O VAL R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 207 removed outlier: 3.732A pdb=" N LEU R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 252 removed outlier: 4.603A pdb=" N GLY R 238 " --> pdb=" O GLY R 234 " (cutoff:3.500A) Proline residue: R 239 - end of helix removed outlier: 4.192A pdb=" N GLU R 252 " --> pdb=" O VAL R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 282 removed outlier: 3.701A pdb=" N LEU R 265 " --> pdb=" O THR R 261 " (cutoff:3.500A) Proline residue: R 277 - end of helix Processing helix chain 'R' and resid 284 through 289 removed outlier: 3.522A pdb=" N THR R 288 " --> pdb=" O ASP R 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.695A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.216A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.013A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.510A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.672A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.515A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.056A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.657A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.621A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.520A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1156 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: 2.29 Time building geometry restraints manager: 2.90 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: 2581 1.34 - 1.45: 1237 1.45 - 1.57: 4298 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 8181 Sorted by residual: bond pdb=" C1 H8I R 401 " pdb=" N2 H8I R 401 " ideal model delta sigma weight residual 1.352 1.407 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" C3 H8I R 401 " pdb=" N1 H8I R 401 " ideal model delta sigma weight residual 1.309 1.355 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C7 H8I R 401 " pdb=" O1 H8I R 401 " ideal model delta sigma weight residual 1.365 1.403 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C7 H8I R 401 " pdb=" C8 H8I R 401 " ideal model delta sigma weight residual 1.390 1.424 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C2 H8I R 401 " pdb=" C3 H8I R 401 " ideal model delta sigma weight residual 1.396 1.424 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 8176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 10977 2.76 - 5.52: 106 5.52 - 8.29: 20 8.29 - 11.05: 3 11.05 - 13.81: 1 Bond angle restraints: 11107 Sorted by residual: angle pdb=" C2 H8I R 401 " pdb=" C1 H8I R 401 " pdb=" N2 H8I R 401 " ideal model delta sigma weight residual 117.71 131.52 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.63 3.57 9.60e-01 1.09e+00 1.39e+01 angle pdb=" N GLN B 9 " pdb=" CA GLN B 9 " pdb=" CB GLN B 9 " ideal model delta sigma weight residual 110.28 115.61 -5.33 1.55e+00 4.16e-01 1.18e+01 angle pdb=" C3 H8I R 401 " pdb=" O1 H8I R 401 " pdb=" C7 H8I R 401 " ideal model delta sigma weight residual 119.25 129.24 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C PRO A 321 " pdb=" N GLU A 322 " pdb=" CA GLU A 322 " ideal model delta sigma weight residual 121.54 127.76 -6.22 1.91e+00 2.74e-01 1.06e+01 ... (remaining 11102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4501 17.64 - 35.28: 326 35.28 - 52.92: 51 52.92 - 70.55: 9 70.55 - 88.19: 4 Dihedral angle restraints: 4891 sinusoidal: 1920 harmonic: 2971 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 50.97 42.03 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PRO B 194 " pdb=" C PRO B 194 " pdb=" N ASP B 195 " pdb=" CA ASP B 195 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 4888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 796 0.037 - 0.074: 307 0.074 - 0.111: 112 0.111 - 0.148: 22 0.148 - 0.185: 5 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA GLN A 31 " pdb=" N GLN A 31 " pdb=" C GLN A 31 " pdb=" CB GLN A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB THR B 223 " pdb=" CA THR B 223 " pdb=" OG1 THR B 223 " pdb=" CG2 THR B 223 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 1239 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 134 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO R 135 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 135 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 135 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 228 " -0.181 9.50e-02 1.11e+02 8.14e-02 4.28e+00 pdb=" NE ARG A 228 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 228 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 228 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 228 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO A 321 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.026 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 471 2.73 - 3.27: 7767 3.27 - 3.82: 13060 3.82 - 4.36: 14743 4.36 - 4.90: 26436 Nonbonded interactions: 62477 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.192 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.194 3.040 nonbonded pdb=" O MET B 325 " pdb=" OD1 ASN B 340 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.246 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.273 3.040 ... (remaining 62472 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=0.38 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.530 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 0.055 8181 Z= 0.240 Angle : 0.745 13.809 11107 Z= 0.371 Chirality : 0.046 0.185 1242 Planarity : 0.005 0.081 1431 Dihedral : 12.535 88.193 2966 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.37 (0.26), residues: 1016 helix: 1.49 (0.25), residues: 399 sheet: -0.69 (0.34), residues: 215 loop : -1.79 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 281 HIS 0.007 0.001 HIS A 220 PHE 0.023 0.002 PHE A 212 TYR 0.014 0.001 TYR B 59 ARG 0.008 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.924 Fit side-chains REVERT: A 21 GLU cc_start: 0.6377 (mm-30) cc_final: 0.6096 (mm-30) REVERT: A 209 GLU cc_start: 0.6027 (tp30) cc_final: 0.5750 (tp30) REVERT: A 210 THR cc_start: 0.8203 (p) cc_final: 0.7399 (m) REVERT: A 228 ARG cc_start: 0.7563 (ptm-80) cc_final: 0.7231 (ptt180) REVERT: A 299 GLU cc_start: 0.7339 (tp30) cc_final: 0.6947 (tp30) REVERT: A 392 GLU cc_start: 0.7115 (tp30) cc_final: 0.6546 (tp30) REVERT: B 83 ASP cc_start: 0.7800 (t0) cc_final: 0.7335 (t70) REVERT: B 148 CYS cc_start: 0.7185 (t) cc_final: 0.6952 (t) REVERT: B 170 ASP cc_start: 0.6873 (t0) cc_final: 0.6569 (t0) REVERT: B 197 ARG cc_start: 0.7076 (mtp180) cc_final: 0.6439 (mtp180) REVERT: B 214 ARG cc_start: 0.7301 (ptt90) cc_final: 0.6357 (ptt90) REVERT: G 21 MET cc_start: 0.6969 (tmm) cc_final: 0.6692 (tmm) REVERT: N 31 ASN cc_start: 0.8264 (m110) cc_final: 0.8024 (m110) REVERT: N 43 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7855 (mmmt) REVERT: R 248 VAL cc_start: 0.7218 (t) cc_final: 0.6969 (t) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3030 time to fit residues: 77.3110 Evaluate side-chains 181 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 213 GLN B 119 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8181 Z= 0.324 Angle : 0.679 12.137 11107 Z= 0.333 Chirality : 0.046 0.168 1242 Planarity : 0.005 0.056 1431 Dihedral : 5.337 65.437 1145 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.42 % Allowed : 9.72 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1016 helix: 1.92 (0.26), residues: 387 sheet: -0.45 (0.33), residues: 218 loop : -1.74 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.021 0.002 PHE N 108 TYR 0.019 0.002 TYR N 60 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 1.043 Fit side-chains REVERT: A 21 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6162 (mm-30) REVERT: A 209 GLU cc_start: 0.6186 (tp30) cc_final: 0.5848 (tp30) REVERT: A 210 THR cc_start: 0.7915 (p) cc_final: 0.7293 (m) REVERT: A 230 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6555 (mm-30) REVERT: A 392 GLU cc_start: 0.7113 (tp30) cc_final: 0.6840 (tp30) REVERT: B 40 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7816 (p) REVERT: B 48 ARG cc_start: 0.7966 (mmt180) cc_final: 0.7681 (mmt-90) REVERT: B 52 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7637 (mtt90) REVERT: B 127 LYS cc_start: 0.7966 (mptt) cc_final: 0.7712 (mptt) REVERT: B 197 ARG cc_start: 0.7079 (mtp180) cc_final: 0.6672 (mtp180) REVERT: B 214 ARG cc_start: 0.7273 (ptt90) cc_final: 0.6395 (ptt90) REVERT: B 327 VAL cc_start: 0.7970 (t) cc_final: 0.7732 (p) REVERT: G 21 MET cc_start: 0.6990 (tmm) cc_final: 0.6753 (tmm) REVERT: N 31 ASN cc_start: 0.8331 (m110) cc_final: 0.8054 (m-40) REVERT: N 43 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7855 (mmmt) outliers start: 12 outliers final: 8 residues processed: 195 average time/residue: 0.3166 time to fit residues: 76.9936 Evaluate side-chains 194 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 170 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8181 Z= 0.249 Angle : 0.626 12.539 11107 Z= 0.305 Chirality : 0.044 0.160 1242 Planarity : 0.005 0.052 1431 Dihedral : 5.155 65.682 1145 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.90 % Allowed : 12.68 % Favored : 85.43 % 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: 0.20 (0.26), residues: 1016 helix: 2.16 (0.26), residues: 387 sheet: -0.34 (0.33), residues: 223 loop : -1.66 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.018 0.002 PHE B 241 TYR 0.014 0.001 TYR A 339 ARG 0.007 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6450 (mm-30) cc_final: 0.6152 (mm-30) REVERT: A 209 GLU cc_start: 0.6277 (tp30) cc_final: 0.5932 (tp30) REVERT: A 210 THR cc_start: 0.7951 (p) cc_final: 0.7368 (m) REVERT: A 392 GLU cc_start: 0.7142 (tp30) cc_final: 0.6867 (tp30) REVERT: B 40 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7852 (p) REVERT: B 48 ARG cc_start: 0.7941 (mmt180) cc_final: 0.7657 (mmt-90) REVERT: B 126 LEU cc_start: 0.8127 (mm) cc_final: 0.7903 (mp) REVERT: B 197 ARG cc_start: 0.7069 (mtp180) cc_final: 0.6595 (mtp180) REVERT: B 223 THR cc_start: 0.8109 (t) cc_final: 0.7890 (p) REVERT: B 292 PHE cc_start: 0.7748 (m-10) cc_final: 0.7413 (m-80) REVERT: B 327 VAL cc_start: 0.7988 (t) cc_final: 0.7744 (p) REVERT: G 21 MET cc_start: 0.7006 (tmm) cc_final: 0.6771 (tmm) REVERT: N 31 ASN cc_start: 0.8283 (m110) cc_final: 0.8058 (m-40) REVERT: N 43 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7854 (mmmt) REVERT: R 80 ARG cc_start: 0.6971 (ttm-80) cc_final: 0.6675 (ttm-80) outliers start: 16 outliers final: 11 residues processed: 204 average time/residue: 0.2832 time to fit residues: 72.1911 Evaluate side-chains 204 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 80 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 119 ASN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.003 0.032 8181 Z= 0.164 Angle : 0.582 10.703 11107 Z= 0.282 Chirality : 0.042 0.153 1242 Planarity : 0.004 0.050 1431 Dihedral : 4.910 65.608 1145 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.78 % Allowed : 14.45 % Favored : 83.77 % 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: 0.36 (0.26), residues: 1016 helix: 2.25 (0.26), residues: 394 sheet: -0.26 (0.33), residues: 216 loop : -1.56 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.001 PHE B 241 TYR 0.013 0.001 TYR A 339 ARG 0.005 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.930 Fit side-chains REVERT: A 21 GLU cc_start: 0.6394 (mm-30) cc_final: 0.6082 (mm-30) REVERT: A 209 GLU cc_start: 0.6297 (tp30) cc_final: 0.5961 (tp30) REVERT: A 210 THR cc_start: 0.7886 (p) cc_final: 0.7337 (m) REVERT: A 392 GLU cc_start: 0.7129 (tp30) cc_final: 0.6848 (tp30) REVERT: B 48 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7667 (mmt-90) REVERT: B 126 LEU cc_start: 0.7767 (mm) cc_final: 0.7407 (mt) REVERT: B 223 THR cc_start: 0.8061 (t) cc_final: 0.7836 (p) REVERT: B 292 PHE cc_start: 0.7705 (m-10) cc_final: 0.7367 (m-80) REVERT: G 21 MET cc_start: 0.6942 (tmm) cc_final: 0.6712 (tmm) REVERT: N 31 ASN cc_start: 0.8229 (m110) cc_final: 0.7909 (m-40) REVERT: N 43 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7839 (mmmt) REVERT: N 60 TYR cc_start: 0.8473 (m-80) cc_final: 0.8196 (m-80) REVERT: R 112 MET cc_start: 0.7321 (mmt) cc_final: 0.6955 (mpp) outliers start: 15 outliers final: 8 residues processed: 201 average time/residue: 0.2724 time to fit residues: 68.3977 Evaluate side-chains 199 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 0.0870 chunk 39 optimal weight: 0.0370 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.0070 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN R 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8181 Z= 0.137 Angle : 0.561 9.309 11107 Z= 0.270 Chirality : 0.041 0.142 1242 Planarity : 0.004 0.050 1431 Dihedral : 4.726 65.843 1145 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.90 % Allowed : 15.52 % Favored : 82.58 % 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: 0.56 (0.27), residues: 1016 helix: 2.40 (0.26), residues: 394 sheet: -0.19 (0.34), residues: 217 loop : -1.41 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.006 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.870 Fit side-chains REVERT: B 61 MET cc_start: 0.7132 (ppp) cc_final: 0.6857 (ppp) REVERT: B 126 LEU cc_start: 0.7644 (mm) cc_final: 0.7360 (mt) REVERT: B 214 ARG cc_start: 0.7425 (ptt90) cc_final: 0.7184 (ptt90) REVERT: B 223 THR cc_start: 0.8012 (t) cc_final: 0.7807 (p) REVERT: B 292 PHE cc_start: 0.7675 (m-10) cc_final: 0.7332 (m-80) REVERT: G 21 MET cc_start: 0.6929 (tmm) cc_final: 0.6689 (tmm) REVERT: N 31 ASN cc_start: 0.8198 (m110) cc_final: 0.7904 (m-40) REVERT: N 43 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7872 (mmmt) REVERT: N 60 TYR cc_start: 0.8457 (m-80) cc_final: 0.8244 (m-80) REVERT: R 95 SER cc_start: 0.7397 (p) cc_final: 0.7178 (t) REVERT: R 112 MET cc_start: 0.7305 (mmt) cc_final: 0.6907 (mpp) outliers start: 16 outliers final: 11 residues processed: 201 average time/residue: 0.2813 time to fit residues: 71.0340 Evaluate side-chains 195 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8181 Z= 0.318 Angle : 0.647 12.731 11107 Z= 0.315 Chirality : 0.045 0.151 1242 Planarity : 0.005 0.051 1431 Dihedral : 5.091 66.246 1145 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.49 % Allowed : 17.30 % Favored : 80.21 % 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: 0.48 (0.27), residues: 1016 helix: 2.31 (0.26), residues: 387 sheet: -0.23 (0.33), residues: 233 loop : -1.40 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.019 0.002 PHE B 241 TYR 0.018 0.002 TYR N 60 ARG 0.011 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.881 Fit side-chains REVERT: A 21 GLU cc_start: 0.6471 (mm-30) cc_final: 0.6147 (mm-30) REVERT: A 209 GLU cc_start: 0.6372 (tp30) cc_final: 0.6017 (tp30) REVERT: A 228 ARG cc_start: 0.8053 (ptm-80) cc_final: 0.7431 (ptt180) REVERT: A 392 GLU cc_start: 0.7093 (tp30) cc_final: 0.6822 (tp30) REVERT: B 40 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.7924 (p) REVERT: B 48 ARG cc_start: 0.8079 (mmt-90) cc_final: 0.7765 (mmt-90) REVERT: B 61 MET cc_start: 0.7245 (ppp) cc_final: 0.6857 (ppp) REVERT: B 126 LEU cc_start: 0.7952 (mm) cc_final: 0.7656 (mt) REVERT: B 214 ARG cc_start: 0.7486 (ptt90) cc_final: 0.7204 (ptt90) REVERT: B 219 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7475 (ttm-80) REVERT: B 223 THR cc_start: 0.8092 (t) cc_final: 0.7868 (p) REVERT: B 327 VAL cc_start: 0.8013 (t) cc_final: 0.7783 (p) REVERT: G 21 MET cc_start: 0.6975 (tmm) cc_final: 0.6727 (tmm) REVERT: N 43 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7853 (mmmt) REVERT: R 112 MET cc_start: 0.7338 (mmt) cc_final: 0.6970 (mpp) outliers start: 21 outliers final: 16 residues processed: 201 average time/residue: 0.2653 time to fit residues: 67.8158 Evaluate side-chains 197 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN G 44 HIS N 31 ASN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8181 Z= 0.203 Angle : 0.604 11.441 11107 Z= 0.291 Chirality : 0.042 0.140 1242 Planarity : 0.004 0.052 1431 Dihedral : 4.954 66.768 1145 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.13 % Allowed : 18.60 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 1016 helix: 2.29 (0.26), residues: 394 sheet: -0.19 (0.34), residues: 228 loop : -1.32 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.001 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.848 Fit side-chains REVERT: A 21 GLU cc_start: 0.6435 (mm-30) cc_final: 0.6121 (mm-30) REVERT: A 209 GLU cc_start: 0.6379 (tp30) cc_final: 0.6091 (tp30) REVERT: A 210 THR cc_start: 0.8111 (m) cc_final: 0.7246 (m) REVERT: A 392 GLU cc_start: 0.7113 (tp30) cc_final: 0.6847 (tp30) REVERT: B 40 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7973 (p) REVERT: B 43 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8119 (tp) REVERT: B 61 MET cc_start: 0.7123 (ppp) cc_final: 0.6815 (ppp) REVERT: B 126 LEU cc_start: 0.7865 (mm) cc_final: 0.7561 (mt) REVERT: B 214 ARG cc_start: 0.7496 (ptt90) cc_final: 0.7199 (ptt90) REVERT: B 219 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7387 (ttm-80) REVERT: B 223 THR cc_start: 0.8033 (t) cc_final: 0.7815 (p) REVERT: G 21 MET cc_start: 0.6972 (tmm) cc_final: 0.6724 (tmm) REVERT: N 43 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7882 (mmmt) REVERT: N 60 TYR cc_start: 0.8478 (m-80) cc_final: 0.8198 (m-80) REVERT: R 112 MET cc_start: 0.7308 (mmt) cc_final: 0.6933 (mpp) outliers start: 18 outliers final: 14 residues processed: 188 average time/residue: 0.2502 time to fit residues: 60.3359 Evaluate side-chains 196 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN N 39 GLN N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8181 Z= 0.177 Angle : 0.596 10.521 11107 Z= 0.287 Chirality : 0.042 0.140 1242 Planarity : 0.004 0.054 1431 Dihedral : 4.871 67.779 1145 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.13 % Allowed : 19.31 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 1016 helix: 2.36 (0.26), residues: 394 sheet: -0.13 (0.34), residues: 228 loop : -1.29 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.016 0.001 PHE N 103 TYR 0.012 0.001 TYR A 339 ARG 0.008 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.983 Fit side-chains REVERT: A 21 GLU cc_start: 0.6412 (mm-30) cc_final: 0.6100 (mm-30) REVERT: A 209 GLU cc_start: 0.6381 (tp30) cc_final: 0.6110 (tp30) REVERT: A 210 THR cc_start: 0.8090 (m) cc_final: 0.7303 (m) REVERT: A 228 ARG cc_start: 0.8000 (ptm-80) cc_final: 0.7436 (ptt180) REVERT: A 392 GLU cc_start: 0.7101 (tp30) cc_final: 0.6804 (tp30) REVERT: B 40 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 43 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8112 (tp) REVERT: B 48 ARG cc_start: 0.8094 (mmt-90) cc_final: 0.7767 (mmt-90) REVERT: B 61 MET cc_start: 0.7046 (ppp) cc_final: 0.6798 (ppp) REVERT: B 126 LEU cc_start: 0.7786 (mm) cc_final: 0.7482 (mt) REVERT: B 194 PRO cc_start: 0.8648 (Cg_exo) cc_final: 0.8432 (Cg_endo) REVERT: B 214 ARG cc_start: 0.7499 (ptt90) cc_final: 0.7198 (ptt90) REVERT: B 219 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7318 (ttm-80) REVERT: B 223 THR cc_start: 0.8013 (t) cc_final: 0.7796 (p) REVERT: G 21 MET cc_start: 0.6939 (tmm) cc_final: 0.6716 (tmm) REVERT: N 43 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7873 (mmmt) REVERT: N 60 TYR cc_start: 0.8469 (m-80) cc_final: 0.8142 (m-80) REVERT: R 112 MET cc_start: 0.7303 (mmt) cc_final: 0.6900 (mpp) outliers start: 18 outliers final: 14 residues processed: 193 average time/residue: 0.2618 time to fit residues: 63.9709 Evaluate side-chains 193 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 185 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.0770 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 75 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8181 Z= 0.167 Angle : 0.585 9.730 11107 Z= 0.281 Chirality : 0.042 0.139 1242 Planarity : 0.004 0.050 1431 Dihedral : 4.785 67.219 1145 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.25 % Allowed : 19.19 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 1016 helix: 2.40 (0.26), residues: 394 sheet: -0.12 (0.34), residues: 229 loop : -1.25 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 1.060 Fit side-chains REVERT: A 21 GLU cc_start: 0.6348 (mm-30) cc_final: 0.6054 (mm-30) REVERT: A 209 GLU cc_start: 0.6388 (tp30) cc_final: 0.6119 (tp30) REVERT: A 210 THR cc_start: 0.8012 (m) cc_final: 0.7190 (m) REVERT: A 228 ARG cc_start: 0.7981 (ptm-80) cc_final: 0.7436 (ptt180) REVERT: A 392 GLU cc_start: 0.7111 (tp30) cc_final: 0.6806 (tp30) REVERT: B 40 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.7967 (p) REVERT: B 43 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8105 (tp) REVERT: B 48 ARG cc_start: 0.8084 (mmt-90) cc_final: 0.7771 (mmt-90) REVERT: B 61 MET cc_start: 0.6990 (ppp) cc_final: 0.6764 (ppp) REVERT: B 126 LEU cc_start: 0.7750 (mm) cc_final: 0.7491 (mt) REVERT: B 194 PRO cc_start: 0.8638 (Cg_exo) cc_final: 0.8425 (Cg_endo) REVERT: B 214 ARG cc_start: 0.7508 (ptt90) cc_final: 0.7180 (ptt90) REVERT: B 219 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7348 (ttm-80) REVERT: B 223 THR cc_start: 0.7997 (t) cc_final: 0.7769 (p) REVERT: N 43 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7870 (mmmt) REVERT: N 60 TYR cc_start: 0.8476 (m-80) cc_final: 0.8216 (m-80) REVERT: R 112 MET cc_start: 0.7292 (mmt) cc_final: 0.6889 (mpp) outliers start: 19 outliers final: 14 residues processed: 195 average time/residue: 0.3225 time to fit residues: 81.0546 Evaluate side-chains 200 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN N 31 ASN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8181 Z= 0.184 Angle : 0.614 9.680 11107 Z= 0.292 Chirality : 0.042 0.140 1242 Planarity : 0.004 0.049 1431 Dihedral : 4.754 66.797 1145 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.25 % Allowed : 19.55 % Favored : 78.20 % 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: 0.67 (0.27), residues: 1016 helix: 2.36 (0.26), residues: 394 sheet: -0.11 (0.35), residues: 228 loop : -1.23 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.007 0.000 ARG R 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.938 Fit side-chains REVERT: A 21 GLU cc_start: 0.6372 (mm-30) cc_final: 0.6075 (mm-30) REVERT: A 209 GLU cc_start: 0.6387 (tp30) cc_final: 0.6125 (tp30) REVERT: A 210 THR cc_start: 0.8001 (m) cc_final: 0.7211 (m) REVERT: A 228 ARG cc_start: 0.7992 (ptm-80) cc_final: 0.7588 (ptt180) REVERT: A 392 GLU cc_start: 0.7157 (tp30) cc_final: 0.6888 (tp30) REVERT: B 40 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7945 (p) REVERT: B 43 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8110 (tp) REVERT: B 52 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7432 (mtt90) REVERT: B 61 MET cc_start: 0.7015 (ppp) cc_final: 0.6767 (ppp) REVERT: B 126 LEU cc_start: 0.7761 (mm) cc_final: 0.7497 (mt) REVERT: B 194 PRO cc_start: 0.8642 (Cg_exo) cc_final: 0.8418 (Cg_endo) REVERT: B 214 ARG cc_start: 0.7499 (ptt90) cc_final: 0.7201 (ptt90) REVERT: B 223 THR cc_start: 0.8000 (t) cc_final: 0.7758 (p) REVERT: N 43 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7877 (mmmt) REVERT: N 60 TYR cc_start: 0.8479 (m-80) cc_final: 0.8219 (m-80) REVERT: R 112 MET cc_start: 0.7293 (mmt) cc_final: 0.6888 (mpp) outliers start: 19 outliers final: 16 residues processed: 194 average time/residue: 0.2832 time to fit residues: 69.1640 Evaluate side-chains 201 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.0770 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.0570 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109864 restraints weight = 21285.437| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.80 r_work: 0.3247 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8181 Z= 0.169 Angle : 0.617 10.962 11107 Z= 0.291 Chirality : 0.042 0.143 1242 Planarity : 0.004 0.049 1431 Dihedral : 4.722 66.628 1145 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.25 % Allowed : 19.79 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 1016 helix: 2.40 (0.26), residues: 394 sheet: -0.09 (0.35), residues: 228 loop : -1.20 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.007 0.000 ARG R 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2285.18 seconds wall clock time: 42 minutes 17.62 seconds (2537.62 seconds total)