Starting phenix.real_space_refine on Wed Apr 30 06:17:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7na7_24267/04_2025/7na7_24267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7na7_24267/04_2025/7na7_24267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7na7_24267/04_2025/7na7_24267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7na7_24267/04_2025/7na7_24267.map" model { file = "/net/cci-nas-00/data/ceres_data/7na7_24267/04_2025/7na7_24267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7na7_24267/04_2025/7na7_24267.cif" } resolution = 2.7 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= 0.001 sd= 0.023 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 62 5.16 5 C 5786 2.51 5 N 1526 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2339 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 1 Chain: "L" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1IC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.50, per 1000 atoms: 0.72 Number of scatterers: 9036 At special positions: 0 Unit cell: (87.75, 120.25, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1662 8.00 N 1526 7.00 C 5786 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=2.03 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " 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: 2.34 Conformation dependent library (CDL) restraints added in 1.0 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 1IC L 3 " Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 38.0% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.587A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.359A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.017A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.699A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.697A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 328 through 352 Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.545A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 30 through 44 removed outlier: 4.444A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 40 through 71 removed outlier: 4.142A pdb=" N ALA R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 75 Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 95 through 105 Processing helix chain 'R' and resid 112 through 147 removed outlier: 3.713A pdb=" N GLN R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 155 removed outlier: 3.607A pdb=" N VAL R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 176 removed outlier: 3.570A pdb=" N LEU R 162 " --> pdb=" O GLY R 158 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL R 163 " --> pdb=" O ARG R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 182 Processing helix chain 'R' and resid 191 through 196 removed outlier: 3.771A pdb=" N THR R 195 " --> pdb=" O ASP R 191 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN R 196 " --> pdb=" O PRO R 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 191 through 196' Processing helix chain 'R' and resid 202 through 207 Processing helix chain 'R' and resid 208 through 243 removed outlier: 3.512A pdb=" N SER R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE R 219 " --> pdb=" O TRP R 215 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Proline residue: R 224 - end of helix removed outlier: 3.509A pdb=" N ARG R 243 " --> pdb=" O LEU R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 290 Proline residue: R 278 - end of helix removed outlier: 3.757A pdb=" N PHE R 290 " --> pdb=" O PHE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 325 removed outlier: 4.074A pdb=" N GLN R 299 " --> pdb=" O LEU R 295 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA R 316 " --> pdb=" O PHE R 312 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'R' and resid 327 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.172A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.544A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.518A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.580A 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: 6.733A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.765A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.158A 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: 6.659A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.649A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.856A 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: 4.010A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.100A 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 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.802A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.223A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'N' and resid 146 through 148 removed outlier: 6.345A pdb=" N LEU N 174 " --> pdb=" O TYR N 190 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR N 190 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP N 176 " --> pdb=" O LEU N 188 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1230 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: 2.63 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1446 1.30 - 1.43: 2481 1.43 - 1.56: 5218 1.56 - 1.69: 0 1.69 - 1.82: 88 Bond restraints: 9233 Sorted by residual: bond pdb=" CA SER N 106 " pdb=" CB SER N 106 " ideal model delta sigma weight residual 1.531 1.449 0.082 1.22e-02 6.72e+03 4.51e+01 bond pdb=" C PRO N 107 " pdb=" O PRO N 107 " ideal model delta sigma weight residual 1.234 1.169 0.064 1.14e-02 7.69e+03 3.17e+01 bond pdb=" CA SER N 105 " pdb=" CB SER N 105 " ideal model delta sigma weight residual 1.529 1.447 0.082 1.61e-02 3.86e+03 2.62e+01 bond pdb=" C LEU N 174 " pdb=" O LEU N 174 " ideal model delta sigma weight residual 1.236 1.177 0.058 1.14e-02 7.69e+03 2.62e+01 bond pdb=" C TYR N 175 " pdb=" O TYR N 175 " ideal model delta sigma weight residual 1.234 1.185 0.048 1.17e-02 7.31e+03 1.71e+01 ... (remaining 9228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 12259 3.26 - 6.51: 225 6.51 - 9.77: 19 9.77 - 13.03: 2 13.03 - 16.28: 2 Bond angle restraints: 12507 Sorted by residual: angle pdb=" C 1IC L 3 " pdb=" CA 1IC L 3 " pdb=" CB 1IC L 3 " ideal model delta sigma weight residual 110.50 126.38 -15.88 1.50e+00 4.44e-01 1.12e+02 angle pdb=" C GLN R 302 " pdb=" CA GLN R 302 " pdb=" CB GLN R 302 " ideal model delta sigma weight residual 110.63 126.91 -16.28 1.85e+00 2.92e-01 7.75e+01 angle pdb=" N GLU A 8 " pdb=" CA GLU A 8 " pdb=" C GLU A 8 " ideal model delta sigma weight residual 112.92 103.28 9.64 1.23e+00 6.61e-01 6.14e+01 angle pdb=" C ARG N 191 " pdb=" CA ARG N 191 " pdb=" CB ARG N 191 " ideal model delta sigma weight residual 111.80 122.64 -10.84 1.46e+00 4.69e-01 5.51e+01 angle pdb=" N LEU R 103 " pdb=" CA LEU R 103 " pdb=" C LEU R 103 " ideal model delta sigma weight residual 113.01 105.72 7.29 1.20e+00 6.94e-01 3.69e+01 ... (remaining 12502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 5470 34.69 - 69.38: 85 69.38 - 104.07: 7 104.07 - 138.76: 3 138.76 - 173.45: 4 Dihedral angle restraints: 5569 sinusoidal: 2266 harmonic: 3303 Sorted by residual: dihedral pdb=" C GLN R 302 " pdb=" N GLN R 302 " pdb=" CA GLN R 302 " pdb=" CB GLN R 302 " ideal model delta harmonic sigma weight residual -122.60 -141.66 19.06 0 2.50e+00 1.60e-01 5.81e+01 dihedral pdb=" C ARG N 191 " pdb=" N ARG N 191 " pdb=" CA ARG N 191 " pdb=" CB ARG N 191 " ideal model delta harmonic sigma weight residual -122.60 -140.00 17.40 0 2.50e+00 1.60e-01 4.84e+01 dihedral pdb=" C ASN R 305 " pdb=" N ASN R 305 " pdb=" CA ASN R 305 " pdb=" CB ASN R 305 " ideal model delta harmonic sigma weight residual -122.60 -137.94 15.34 0 2.50e+00 1.60e-01 3.76e+01 ... (remaining 5566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.166: 1416 1.166 - 2.333: 0 2.333 - 3.499: 0 3.499 - 4.665: 0 4.665 - 5.831: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 2.90 -5.83 2.00e-01 2.50e+01 8.50e+02 chirality pdb=" C17 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C16 CLR R 402 " pdb=" C20 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.55 -2.63 5.18 2.00e-01 2.50e+01 6.72e+02 chirality pdb=" CA 1IC L 3 " pdb=" N 1IC L 3 " pdb=" C 1IC L 3 " pdb=" CB 1IC L 3 " both_signs ideal model delta sigma weight residual False -2.48 -1.84 -0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 1415 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU N 174 " 0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C LEU N 174 " -0.091 2.00e-02 2.50e+03 pdb=" O LEU N 174 " 0.035 2.00e-02 2.50e+03 pdb=" N TYR N 175 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 6 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C SER A 6 " 0.075 2.00e-02 2.50e+03 pdb=" O SER A 6 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 7 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL N 147 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO N 148 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO N 148 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO N 148 " -0.039 5.00e-02 4.00e+02 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 566 2.72 - 3.27: 8743 3.27 - 3.81: 14984 3.81 - 4.36: 19413 4.36 - 4.90: 33264 Nonbonded interactions: 76970 Sorted by model distance: nonbonded pdb=" OG1 THR R 76 " pdb=" OD1 ASN R 79 " model vdw 2.178 3.040 nonbonded pdb=" O GLY R 57 " pdb=" ND2 ASN R 61 " model vdw 2.250 3.120 nonbonded pdb=" O MET G 38 " pdb=" OE1 GLU G 42 " model vdw 2.277 3.040 nonbonded pdb=" O PRO R 192 " pdb=" OD1 ASN R 196 " model vdw 2.284 3.040 nonbonded pdb=" O PHE N 32 " pdb=" NH2 ARG N 72 " model vdw 2.322 3.120 ... (remaining 76965 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: 4.640 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: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.360 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 9236 Z= 0.382 Angle : 1.043 16.282 12513 Z= 0.655 Chirality : 0.218 5.831 1418 Planarity : 0.006 0.071 1566 Dihedral : 14.699 173.449 3428 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.61 % Allowed : 3.98 % Favored : 95.41 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 3.03 % 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: 0.32 (0.23), residues: 1119 helix: 0.86 (0.26), residues: 388 sheet: 0.67 (0.28), residues: 298 loop : -0.62 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 176 HIS 0.008 0.001 HIS B 54 PHE 0.019 0.002 PHE R 179 TYR 0.034 0.003 TYR N 102 ARG 0.009 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.17976 ( 437) hydrogen bonds : angle 6.76181 ( 1230) SS BOND : bond 0.00460 ( 3) SS BOND : angle 1.09701 ( 6) covalent geometry : bond 0.00620 ( 9233) covalent geometry : angle 1.04259 (12507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 237 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7165 (m-30) cc_final: 0.6770 (m-30) REVERT: A 186 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6501 (mt-10) REVERT: A 245 GLU cc_start: 0.6504 (tp30) cc_final: 0.6069 (tp30) REVERT: A 316 THR cc_start: 0.8443 (m) cc_final: 0.8046 (p) REVERT: B 137 ARG cc_start: 0.7770 (tpp-160) cc_final: 0.7519 (tpt90) REVERT: N 150 THR cc_start: 0.8011 (t) cc_final: 0.7784 (p) REVERT: R 237 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6751 (ttp80) REVERT: R 283 ARG cc_start: 0.6910 (mtp85) cc_final: 0.6671 (mtt-85) REVERT: R 327 SER cc_start: 0.7871 (t) cc_final: 0.7481 (p) REVERT: L 10 GLN cc_start: 0.5134 (mt0) cc_final: 0.4931 (pm20) outliers start: 6 outliers final: 0 residues processed: 241 average time/residue: 1.0546 time to fit residues: 272.8308 Evaluate side-chains 205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 230 ASN B 295 ASN N 82 GLN N 142 GLN N 179 GLN N 183 GLN R 120 GLN R 302 GLN R 319 ASN L 9 HIS L 10 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111309 restraints weight = 12685.364| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.49 r_work: 0.3371 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9236 Z= 0.166 Angle : 0.783 32.053 12513 Z= 0.365 Chirality : 0.062 1.645 1418 Planarity : 0.005 0.051 1566 Dihedral : 12.058 178.309 1375 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.24 % Allowed : 13.35 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.24), residues: 1119 helix: 1.21 (0.26), residues: 397 sheet: 0.73 (0.28), residues: 295 loop : -0.48 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.006 0.001 HIS B 142 PHE 0.023 0.002 PHE A 189 TYR 0.022 0.001 TYR N 190 ARG 0.007 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 437) hydrogen bonds : angle 4.92557 ( 1230) SS BOND : bond 0.00249 ( 3) SS BOND : angle 0.72743 ( 6) covalent geometry : bond 0.00365 ( 9233) covalent geometry : angle 0.78264 (12507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7888 (m-30) cc_final: 0.7573 (m-30) REVERT: A 29 LYS cc_start: 0.8240 (tttm) cc_final: 0.8008 (tttm) REVERT: A 245 GLU cc_start: 0.7397 (tp30) cc_final: 0.7046 (tp30) REVERT: A 316 THR cc_start: 0.8540 (m) cc_final: 0.8227 (p) REVERT: A 345 LYS cc_start: 0.8549 (mttt) cc_final: 0.8288 (mttt) REVERT: B 111 TYR cc_start: 0.8458 (m-80) cc_final: 0.8248 (m-80) REVERT: B 137 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7874 (tpt90) REVERT: N 4 LEU cc_start: 0.8476 (mt) cc_final: 0.8258 (mt) REVERT: R 142 TYR cc_start: 0.8553 (t80) cc_final: 0.8284 (t80) REVERT: R 150 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7959 (ttm170) REVERT: R 237 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7593 (ttp80) REVERT: L 10 GLN cc_start: 0.6059 (mt0) cc_final: 0.5639 (pp30) outliers start: 22 outliers final: 10 residues processed: 222 average time/residue: 1.1749 time to fit residues: 278.4439 Evaluate side-chains 213 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 92 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 175 GLN B 295 ASN G 17 GLN N 82 GLN N 179 GLN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110211 restraints weight = 12875.115| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.49 r_work: 0.3355 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9236 Z= 0.147 Angle : 0.735 31.577 12513 Z= 0.336 Chirality : 0.063 1.753 1418 Planarity : 0.004 0.054 1566 Dihedral : 11.690 176.165 1375 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.96 % Allowed : 15.49 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.24), residues: 1119 helix: 1.42 (0.26), residues: 389 sheet: 0.62 (0.29), residues: 286 loop : -0.49 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS B 142 PHE 0.017 0.001 PHE A 189 TYR 0.016 0.001 TYR N 190 ARG 0.009 0.001 ARG R 283 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 437) hydrogen bonds : angle 4.65880 ( 1230) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.75291 ( 6) covalent geometry : bond 0.00336 ( 9233) covalent geometry : angle 0.73524 (12507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7916 (m-30) cc_final: 0.7612 (m-30) REVERT: A 243 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8024 (tpp) REVERT: A 245 GLU cc_start: 0.7405 (tp30) cc_final: 0.7063 (tp30) REVERT: A 316 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8281 (p) REVERT: A 324 THR cc_start: 0.7518 (m) cc_final: 0.6863 (p) REVERT: N 4 LEU cc_start: 0.8585 (mt) cc_final: 0.8287 (mt) REVERT: N 192 MET cc_start: 0.8229 (ttp) cc_final: 0.7923 (ttp) REVERT: R 142 TYR cc_start: 0.8548 (t80) cc_final: 0.8272 (t80) REVERT: R 150 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7932 (ttm170) REVERT: R 237 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7593 (ttp80) REVERT: R 283 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7247 (mtt180) REVERT: R 332 VAL cc_start: 0.8561 (p) cc_final: 0.8246 (m) outliers start: 29 outliers final: 11 residues processed: 232 average time/residue: 1.1493 time to fit residues: 285.0494 Evaluate side-chains 219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 239 ASN B 295 ASN N 179 GLN R 186 HIS R 302 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108611 restraints weight = 12752.724| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.47 r_work: 0.3332 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9236 Z= 0.208 Angle : 0.787 32.055 12513 Z= 0.360 Chirality : 0.064 1.712 1418 Planarity : 0.004 0.058 1566 Dihedral : 11.890 178.381 1375 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.67 % Allowed : 15.39 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.24), residues: 1119 helix: 1.26 (0.26), residues: 387 sheet: 0.64 (0.28), residues: 294 loop : -0.55 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.006 0.001 HIS B 142 PHE 0.018 0.002 PHE A 189 TYR 0.014 0.002 TYR R 313 ARG 0.007 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 437) hydrogen bonds : angle 4.76296 ( 1230) SS BOND : bond 0.00390 ( 3) SS BOND : angle 1.08350 ( 6) covalent geometry : bond 0.00493 ( 9233) covalent geometry : angle 0.78647 (12507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7943 (m-30) cc_final: 0.7642 (m-30) REVERT: A 245 GLU cc_start: 0.7326 (tp30) cc_final: 0.7049 (tp30) REVERT: B 150 ARG cc_start: 0.8833 (mmt-90) cc_final: 0.8616 (mpt180) REVERT: B 258 ASP cc_start: 0.7878 (t0) cc_final: 0.7480 (t0) REVERT: N 202 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7693 (ttp-170) REVERT: R 142 TYR cc_start: 0.8556 (t80) cc_final: 0.8326 (t80) REVERT: R 150 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7893 (ttm170) REVERT: R 237 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7581 (ttp80) REVERT: R 283 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7081 (mtt180) REVERT: R 332 VAL cc_start: 0.8561 (p) cc_final: 0.8273 (m) outliers start: 36 outliers final: 21 residues processed: 228 average time/residue: 1.2541 time to fit residues: 304.8309 Evaluate side-chains 223 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 328 LYS Chi-restraints excluded: chain L residue 10 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN B 156 GLN B 239 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110440 restraints weight = 12165.267| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.48 r_work: 0.3348 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9236 Z= 0.203 Angle : 0.775 30.932 12513 Z= 0.354 Chirality : 0.064 1.747 1418 Planarity : 0.004 0.061 1566 Dihedral : 11.781 174.698 1375 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.67 % Allowed : 16.82 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.24), residues: 1119 helix: 1.19 (0.26), residues: 388 sheet: 0.54 (0.28), residues: 296 loop : -0.56 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.002 PHE A 189 TYR 0.014 0.002 TYR R 313 ARG 0.007 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 437) hydrogen bonds : angle 4.77385 ( 1230) SS BOND : bond 0.00515 ( 3) SS BOND : angle 1.46139 ( 6) covalent geometry : bond 0.00486 ( 9233) covalent geometry : angle 0.77447 (12507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 2.648 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7979 (m-30) cc_final: 0.7646 (m-30) REVERT: A 245 GLU cc_start: 0.7326 (tp30) cc_final: 0.7057 (tp30) REVERT: A 260 THR cc_start: 0.8649 (m) cc_final: 0.8375 (p) REVERT: A 324 THR cc_start: 0.7608 (m) cc_final: 0.7029 (p) REVERT: B 258 ASP cc_start: 0.7883 (t0) cc_final: 0.7564 (t0) REVERT: N 4 LEU cc_start: 0.8645 (mt) cc_final: 0.8426 (mt) REVERT: N 140 MET cc_start: 0.8484 (mmm) cc_final: 0.8193 (mmt) REVERT: N 223 ASP cc_start: 0.8301 (m-30) cc_final: 0.8002 (m-30) REVERT: R 82 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8114 (mm) REVERT: R 142 TYR cc_start: 0.8547 (t80) cc_final: 0.8305 (t80) REVERT: R 237 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7546 (ttp80) REVERT: R 270 PHE cc_start: 0.7589 (m-10) cc_final: 0.7343 (m-80) REVERT: R 332 VAL cc_start: 0.8545 (p) cc_final: 0.8283 (m) outliers start: 36 outliers final: 21 residues processed: 225 average time/residue: 1.3071 time to fit residues: 317.1536 Evaluate side-chains 229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 328 LYS Chi-restraints excluded: chain L residue 10 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 156 GLN B 239 ASN B 295 ASN N 82 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110097 restraints weight = 12196.293| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.49 r_work: 0.3346 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9236 Z= 0.202 Angle : 0.776 30.771 12513 Z= 0.354 Chirality : 0.064 1.758 1418 Planarity : 0.004 0.062 1566 Dihedral : 11.760 174.758 1375 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.87 % Allowed : 17.33 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1119 helix: 1.17 (0.26), residues: 388 sheet: 0.53 (0.29), residues: 294 loop : -0.57 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.002 PHE A 189 TYR 0.013 0.002 TYR R 313 ARG 0.011 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 437) hydrogen bonds : angle 4.73992 ( 1230) SS BOND : bond 0.00343 ( 3) SS BOND : angle 1.58894 ( 6) covalent geometry : bond 0.00483 ( 9233) covalent geometry : angle 0.77553 (12507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8017 (m-30) cc_final: 0.7673 (m-30) REVERT: A 243 MET cc_start: 0.8445 (tpp) cc_final: 0.8187 (tpp) REVERT: A 245 GLU cc_start: 0.7311 (tp30) cc_final: 0.7026 (tp30) REVERT: A 260 THR cc_start: 0.8655 (m) cc_final: 0.8387 (p) REVERT: A 324 THR cc_start: 0.7646 (m) cc_final: 0.7050 (p) REVERT: B 42 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.7181 (mmm-85) REVERT: B 150 ARG cc_start: 0.8857 (mmt-90) cc_final: 0.8641 (mpt180) REVERT: B 258 ASP cc_start: 0.7870 (t0) cc_final: 0.7432 (t0) REVERT: N 140 MET cc_start: 0.8498 (mmm) cc_final: 0.8199 (mmt) REVERT: N 202 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8156 (ttp-170) REVERT: R 124 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7186 (mm-30) REVERT: R 142 TYR cc_start: 0.8531 (t80) cc_final: 0.8309 (t80) REVERT: R 237 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7577 (ttp80) REVERT: R 332 VAL cc_start: 0.8542 (p) cc_final: 0.8288 (m) outliers start: 38 outliers final: 23 residues processed: 223 average time/residue: 1.1853 time to fit residues: 283.2510 Evaluate side-chains 226 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 202 ARG Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 328 LYS Chi-restraints excluded: chain L residue 10 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN B 239 ASN N 82 GLN N 179 GLN R 186 HIS L 9 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109438 restraints weight = 12411.177| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.51 r_work: 0.3350 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9236 Z= 0.183 Angle : 0.770 30.756 12513 Z= 0.348 Chirality : 0.064 1.763 1418 Planarity : 0.004 0.063 1566 Dihedral : 11.757 175.103 1375 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.57 % Allowed : 17.64 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1119 helix: 1.28 (0.27), residues: 381 sheet: 0.51 (0.28), residues: 292 loop : -0.57 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS L 9 PHE 0.018 0.002 PHE A 189 TYR 0.013 0.001 TYR R 313 ARG 0.010 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 437) hydrogen bonds : angle 4.70367 ( 1230) SS BOND : bond 0.00310 ( 3) SS BOND : angle 1.30085 ( 6) covalent geometry : bond 0.00435 ( 9233) covalent geometry : angle 0.76972 (12507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8021 (m-30) cc_final: 0.7677 (m-30) REVERT: A 243 MET cc_start: 0.8441 (tpp) cc_final: 0.8210 (tpp) REVERT: A 245 GLU cc_start: 0.7288 (tp30) cc_final: 0.7006 (tp30) REVERT: A 324 THR cc_start: 0.7617 (m) cc_final: 0.7031 (p) REVERT: B 215 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6705 (pp20) REVERT: B 258 ASP cc_start: 0.7887 (t0) cc_final: 0.7623 (t0) REVERT: N 192 MET cc_start: 0.8241 (ttp) cc_final: 0.7997 (ttp) REVERT: N 202 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8077 (ttp-170) REVERT: R 124 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7180 (mm-30) REVERT: R 142 TYR cc_start: 0.8525 (t80) cc_final: 0.8317 (t80) REVERT: R 237 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7574 (ttp80) REVERT: R 332 VAL cc_start: 0.8549 (p) cc_final: 0.8296 (m) outliers start: 35 outliers final: 25 residues processed: 216 average time/residue: 1.1609 time to fit residues: 268.3903 Evaluate side-chains 227 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 202 ARG Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 328 LYS Chi-restraints excluded: chain L residue 10 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 0.1980 chunk 96 optimal weight: 0.0980 chunk 103 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN B 239 ASN B 293 ASN N 82 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110532 restraints weight = 12480.621| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.52 r_work: 0.3365 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9236 Z= 0.139 Angle : 0.742 30.749 12513 Z= 0.333 Chirality : 0.063 1.766 1418 Planarity : 0.004 0.062 1566 Dihedral : 11.703 175.804 1375 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.85 % Allowed : 19.16 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1119 helix: 1.45 (0.27), residues: 379 sheet: 0.35 (0.29), residues: 284 loop : -0.46 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE A 189 TYR 0.014 0.001 TYR N 190 ARG 0.011 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 437) hydrogen bonds : angle 4.59114 ( 1230) SS BOND : bond 0.00238 ( 3) SS BOND : angle 1.11072 ( 6) covalent geometry : bond 0.00323 ( 9233) covalent geometry : angle 0.74180 (12507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8023 (m-30) cc_final: 0.7674 (m-30) REVERT: A 243 MET cc_start: 0.8428 (tpp) cc_final: 0.8193 (tpp) REVERT: A 245 GLU cc_start: 0.7287 (tp30) cc_final: 0.6991 (tp30) REVERT: A 324 THR cc_start: 0.7555 (m) cc_final: 0.6972 (p) REVERT: B 42 ARG cc_start: 0.7493 (mmm-85) cc_final: 0.7219 (mmm-85) REVERT: B 150 ARG cc_start: 0.8854 (mmt-90) cc_final: 0.8567 (mpt180) REVERT: N 140 MET cc_start: 0.8438 (mmm) cc_final: 0.8111 (mmt) REVERT: N 202 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8075 (ttp-170) REVERT: R 124 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7263 (mm-30) REVERT: R 142 TYR cc_start: 0.8519 (t80) cc_final: 0.8316 (t80) REVERT: R 237 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7583 (ttp80) REVERT: R 332 VAL cc_start: 0.8540 (p) cc_final: 0.8284 (m) outliers start: 28 outliers final: 19 residues processed: 212 average time/residue: 1.1288 time to fit residues: 256.1172 Evaluate side-chains 215 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 202 ARG Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 0.9990 chunk 95 optimal weight: 0.0470 chunk 24 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 111 optimal weight: 0.0000 chunk 92 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN B 239 ASN B 293 ASN N 82 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112797 restraints weight = 12311.209| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.54 r_work: 0.3372 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9236 Z= 0.128 Angle : 0.737 30.756 12513 Z= 0.329 Chirality : 0.063 1.766 1418 Planarity : 0.004 0.063 1566 Dihedral : 11.688 176.469 1375 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.65 % Allowed : 19.37 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1119 helix: 1.55 (0.27), residues: 379 sheet: 0.28 (0.28), residues: 290 loop : -0.41 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE R 309 TYR 0.013 0.001 TYR N 190 ARG 0.011 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 437) hydrogen bonds : angle 4.51745 ( 1230) SS BOND : bond 0.00219 ( 3) SS BOND : angle 1.00240 ( 6) covalent geometry : bond 0.00293 ( 9233) covalent geometry : angle 0.73650 (12507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7999 (m-30) cc_final: 0.7632 (m-30) REVERT: A 197 LYS cc_start: 0.8268 (mtpm) cc_final: 0.8006 (mtpp) REVERT: A 243 MET cc_start: 0.8439 (tpp) cc_final: 0.8162 (tpp) REVERT: A 245 GLU cc_start: 0.7299 (tp30) cc_final: 0.7035 (tp30) REVERT: A 324 THR cc_start: 0.7530 (m) cc_final: 0.6940 (p) REVERT: B 215 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6680 (pp20) REVERT: N 140 MET cc_start: 0.8415 (mmm) cc_final: 0.8198 (mmt) REVERT: N 202 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8049 (ttp-170) REVERT: R 142 TYR cc_start: 0.8519 (t80) cc_final: 0.8319 (t80) REVERT: R 150 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7859 (ttm170) REVERT: R 237 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7595 (ttp80) REVERT: R 332 VAL cc_start: 0.8533 (p) cc_final: 0.8281 (m) outliers start: 26 outliers final: 19 residues processed: 207 average time/residue: 1.1922 time to fit residues: 263.3137 Evaluate side-chains 219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 202 ARG Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 21 optimal weight: 0.0470 chunk 97 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 156 GLN B 239 ASN B 293 ASN N 82 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108888 restraints weight = 12813.649| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.51 r_work: 0.3330 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9236 Z= 0.170 Angle : 0.771 30.779 12513 Z= 0.346 Chirality : 0.064 1.763 1418 Planarity : 0.004 0.063 1566 Dihedral : 11.754 176.893 1375 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.45 % Allowed : 19.78 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.54 (0.25), residues: 1119 helix: 1.46 (0.27), residues: 379 sheet: 0.32 (0.29), residues: 282 loop : -0.48 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.002 PHE A 189 TYR 0.013 0.001 TYR R 313 ARG 0.013 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 437) hydrogen bonds : angle 4.60350 ( 1230) SS BOND : bond 0.00279 ( 3) SS BOND : angle 1.23093 ( 6) covalent geometry : bond 0.00402 ( 9233) covalent geometry : angle 0.77029 (12507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7992 (m-30) cc_final: 0.7651 (m-30) REVERT: A 197 LYS cc_start: 0.8297 (mtpm) cc_final: 0.7997 (mtpp) REVERT: A 243 MET cc_start: 0.8430 (tpp) cc_final: 0.8155 (tpp) REVERT: A 245 GLU cc_start: 0.7270 (tp30) cc_final: 0.7007 (tp30) REVERT: A 324 THR cc_start: 0.7661 (m) cc_final: 0.7038 (p) REVERT: B 215 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6516 (pp20) REVERT: B 304 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6625 (tmm-80) REVERT: N 140 MET cc_start: 0.8451 (mmm) cc_final: 0.8181 (mmt) REVERT: N 202 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8049 (ttp-170) REVERT: R 142 TYR cc_start: 0.8522 (t80) cc_final: 0.8320 (t80) REVERT: R 237 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7540 (ttp80) REVERT: R 332 VAL cc_start: 0.8553 (p) cc_final: 0.8311 (m) outliers start: 24 outliers final: 18 residues processed: 209 average time/residue: 1.2134 time to fit residues: 270.3748 Evaluate side-chains 220 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 202 ARG Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN B 239 ASN B 293 ASN N 82 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109236 restraints weight = 12744.700| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.51 r_work: 0.3336 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9236 Z= 0.154 Angle : 0.753 30.773 12513 Z= 0.338 Chirality : 0.063 1.766 1418 Planarity : 0.004 0.063 1566 Dihedral : 11.745 177.213 1375 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.55 % Allowed : 19.67 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1119 helix: 1.49 (0.27), residues: 379 sheet: 0.21 (0.28), residues: 292 loop : -0.39 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE A 189 TYR 0.012 0.001 TYR N 190 ARG 0.011 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 437) hydrogen bonds : angle 4.58157 ( 1230) SS BOND : bond 0.00240 ( 3) SS BOND : angle 1.09191 ( 6) covalent geometry : bond 0.00363 ( 9233) covalent geometry : angle 0.75262 (12507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7851.07 seconds wall clock time: 136 minutes 18.55 seconds (8178.55 seconds total)