Starting phenix.real_space_refine on Thu Feb 13 18:33:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7na7_24267/02_2025/7na7_24267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7na7_24267/02_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_24267/02_2025/7na7_24267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7na7_24267/02_2025/7na7_24267.map" model { file = "/net/cci-nas-00/data/ceres_data/7na7_24267/02_2025/7na7_24267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7na7_24267/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.37, per 1000 atoms: 0.70 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: 2.56 Conformation dependent library (CDL) restraints added in 1.2 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: 0.90 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: 2.89 Time building geometry restraints manager: 2.75 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: 5.250 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.000 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.190 ------------------------------------------------------------------------------- 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 9233 Z= 0.402 Angle : 1.043 16.282 12507 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 *********************** 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 : 0.939 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: 1.1538 time to fit residues: 298.0185 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 : 1.050 ------------------------------------------------------------------------------- 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 = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111308 restraints weight = 12685.364| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.48 r_work: 0.3370 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 9233 Z= 0.235 Angle : 0.783 32.053 12507 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 *********************** 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 : 0.970 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7907 (m-30) cc_final: 0.7591 (m-30) REVERT: A 29 LYS cc_start: 0.8238 (tttm) cc_final: 0.8004 (tttm) REVERT: A 245 GLU cc_start: 0.7391 (tp30) cc_final: 0.7040 (tp30) REVERT: A 316 THR cc_start: 0.8540 (m) cc_final: 0.8228 (p) REVERT: A 341 ASP cc_start: 0.8111 (t0) cc_final: 0.7911 (t0) REVERT: A 345 LYS cc_start: 0.8545 (mttt) cc_final: 0.8282 (mttt) REVERT: B 111 TYR cc_start: 0.8462 (m-80) cc_final: 0.8251 (m-80) REVERT: B 137 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7873 (tpt90) REVERT: N 4 LEU cc_start: 0.8476 (mt) cc_final: 0.8259 (mt) REVERT: R 142 TYR cc_start: 0.8555 (t80) cc_final: 0.8286 (t80) REVERT: R 150 ARG cc_start: 0.8188 (ttm110) cc_final: 0.7960 (ttm170) REVERT: R 237 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7590 (ttp80) REVERT: L 10 GLN cc_start: 0.6061 (mt0) cc_final: 0.5635 (pp30) outliers start: 22 outliers final: 10 residues processed: 222 average time/residue: 1.2120 time to fit residues: 287.0962 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 : 1.129 ------------------------------------------------------------------------------- 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: 0.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 92 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 295 ASN G 17 GLN N 82 GLN N 179 GLN L 9 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110477 restraints weight = 12863.798| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.49 r_work: 0.3358 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9233 Z= 0.206 Angle : 0.733 31.320 12507 Z= 0.333 Chirality : 0.062 1.716 1418 Planarity : 0.004 0.049 1566 Dihedral : 11.629 175.063 1375 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.75 % Allowed : 15.70 % 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: 0.69 (0.24), residues: 1119 helix: 1.45 (0.26), residues: 386 sheet: 0.60 (0.29), residues: 286 loop : -0.46 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 109 HIS 0.006 0.001 HIS B 142 PHE 0.017 0.001 PHE R 309 TYR 0.015 0.001 TYR N 190 ARG 0.006 0.001 ARG A 32 *********************** 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 243 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7921 (m-30) cc_final: 0.7608 (m-30) REVERT: A 243 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8081 (tpp) REVERT: A 245 GLU cc_start: 0.7399 (tp30) cc_final: 0.7079 (tp30) REVERT: A 324 THR cc_start: 0.7511 (m) cc_final: 0.6856 (p) REVERT: A 341 ASP cc_start: 0.8011 (t0) cc_final: 0.7773 (t0) REVERT: N 4 LEU cc_start: 0.8605 (mt) cc_final: 0.8299 (mt) REVERT: N 179 GLN cc_start: 0.8561 (tt0) cc_final: 0.8355 (tt0) REVERT: N 202 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7592 (ttp-170) REVERT: R 142 TYR cc_start: 0.8545 (t80) cc_final: 0.8274 (t80) REVERT: R 150 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7913 (ttm170) REVERT: R 237 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7602 (ttp80) REVERT: R 283 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7371 (mtt180) REVERT: R 332 VAL cc_start: 0.8567 (p) cc_final: 0.8254 (m) outliers start: 27 outliers final: 9 residues processed: 228 average time/residue: 1.1746 time to fit residues: 286.3521 Evaluate side-chains 213 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.9990 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- 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 155 ASN B 156 GLN B 220 GLN B 239 ASN B 295 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS R 302 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110957 restraints weight = 12217.413| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.48 r_work: 0.3355 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9233 Z= 0.302 Angle : 0.775 31.213 12507 Z= 0.353 Chirality : 0.064 1.727 1418 Planarity : 0.004 0.058 1566 Dihedral : 11.755 177.204 1375 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.36 % Allowed : 15.80 % Favored : 80.84 % 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: 0.61 (0.24), residues: 1119 helix: 1.34 (0.26), residues: 388 sheet: 0.62 (0.28), residues: 295 loop : -0.52 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.006 0.001 HIS B 142 PHE 0.018 0.002 PHE A 189 TYR 0.014 0.001 TYR R 313 ARG 0.006 0.001 ARG A 32 *********************** 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 248 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7995 (m-30) cc_final: 0.7670 (m-30) REVERT: A 245 GLU cc_start: 0.7359 (tp30) cc_final: 0.7071 (tp30) REVERT: B 150 ARG cc_start: 0.8853 (mmt-90) cc_final: 0.8639 (mpt180) REVERT: B 258 ASP cc_start: 0.7903 (t0) cc_final: 0.7515 (t0) REVERT: N 150 THR cc_start: 0.8198 (t) cc_final: 0.7979 (p) REVERT: R 124 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7292 (mm-30) REVERT: R 142 TYR cc_start: 0.8555 (t80) cc_final: 0.8320 (t80) REVERT: R 150 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7900 (ttm170) REVERT: R 237 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7569 (ttp80) REVERT: R 283 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7112 (mtt180) REVERT: R 332 VAL cc_start: 0.8555 (p) cc_final: 0.8263 (m) outliers start: 33 outliers final: 22 residues processed: 229 average time/residue: 1.2252 time to fit residues: 299.3587 Evaluate side-chains 224 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 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 149 LEU 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: 0.0980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 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 = 0.3642 r_free = 0.3642 target = 0.122869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110481 restraints weight = 12258.438| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.48 r_work: 0.3361 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9233 Z= 0.256 Angle : 0.748 30.909 12507 Z= 0.338 Chirality : 0.063 1.755 1418 Planarity : 0.004 0.059 1566 Dihedral : 11.751 176.005 1375 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.67 % Allowed : 16.51 % Favored : 79.82 % 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: 0.62 (0.24), residues: 1119 helix: 1.46 (0.26), residues: 381 sheet: 0.50 (0.29), residues: 296 loop : -0.51 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.002 PHE A 189 TYR 0.013 0.001 TYR N 190 ARG 0.008 0.000 ARG A 32 *********************** 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 238 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7979 (m-30) cc_final: 0.7634 (m-30) REVERT: A 243 MET cc_start: 0.8481 (tpp) cc_final: 0.8243 (tpp) REVERT: A 245 GLU cc_start: 0.7352 (tp30) cc_final: 0.7077 (tp30) REVERT: B 258 ASP cc_start: 0.7877 (t0) cc_final: 0.7574 (t0) REVERT: N 202 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8111 (ttp-170) REVERT: R 82 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8032 (mm) REVERT: R 124 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7304 (mm-30) REVERT: R 142 TYR cc_start: 0.8545 (t80) cc_final: 0.8298 (t80) REVERT: R 150 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7875 (ttm170) REVERT: R 237 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7554 (ttp80) REVERT: R 283 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7123 (mtt180) REVERT: R 332 VAL cc_start: 0.8550 (p) cc_final: 0.8279 (m) outliers start: 36 outliers final: 20 residues processed: 221 average time/residue: 1.2280 time to fit residues: 289.9293 Evaluate side-chains 223 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 A residue 332 VAL Chi-restraints excluded: chain B residue 52 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 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 82 LEU Chi-restraints excluded: chain R residue 88 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 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 = 0.3643 r_free = 0.3643 target = 0.122964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110519 restraints weight = 12290.719| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.49 r_work: 0.3360 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9233 Z= 0.241 Angle : 0.741 30.840 12507 Z= 0.334 Chirality : 0.063 1.764 1418 Planarity : 0.004 0.060 1566 Dihedral : 11.774 176.753 1375 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.16 % Allowed : 17.74 % Favored : 79.10 % 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: 1.50 (0.26), residues: 381 sheet: 0.44 (0.29), residues: 285 loop : -0.46 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.002 PHE A 189 TYR 0.012 0.001 TYR R 313 ARG 0.009 0.001 ARG A 32 *********************** 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 235 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8011 (m-30) cc_final: 0.7657 (m-30) REVERT: A 243 MET cc_start: 0.8466 (tpp) cc_final: 0.8232 (tpp) REVERT: A 245 GLU cc_start: 0.7328 (tp30) cc_final: 0.7037 (tp30) REVERT: A 260 THR cc_start: 0.8645 (m) cc_final: 0.8386 (p) REVERT: B 150 ARG cc_start: 0.8849 (mmt-90) cc_final: 0.8642 (mpt180) REVERT: B 258 ASP cc_start: 0.7880 (t0) cc_final: 0.7622 (t0) REVERT: N 142 GLN cc_start: 0.8671 (mt0) cc_final: 0.8455 (mt0) REVERT: N 202 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8049 (ttp-170) REVERT: R 82 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8066 (mm) REVERT: R 124 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7326 (mm-30) REVERT: R 142 TYR cc_start: 0.8539 (t80) cc_final: 0.8309 (t80) REVERT: R 237 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7338 (ttp80) REVERT: R 241 ARG cc_start: 0.6673 (ttm110) cc_final: 0.6111 (ttm110) REVERT: R 270 PHE cc_start: 0.7610 (m-10) cc_final: 0.7372 (m-80) REVERT: R 283 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7119 (mtt180) REVERT: R 332 VAL cc_start: 0.8539 (p) cc_final: 0.8277 (m) outliers start: 31 outliers final: 20 residues processed: 219 average time/residue: 1.2174 time to fit residues: 284.4452 Evaluate side-chains 229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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 202 ARG 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 149 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 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 = 0.123067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110509 restraints weight = 12415.721| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.51 r_work: 0.3362 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9233 Z= 0.241 Angle : 0.747 30.827 12507 Z= 0.335 Chirality : 0.064 1.766 1418 Planarity : 0.004 0.061 1566 Dihedral : 11.818 177.603 1375 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.36 % Allowed : 18.14 % Favored : 78.49 % 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: 0.62 (0.25), residues: 1119 helix: 1.50 (0.26), residues: 381 sheet: 0.38 (0.29), residues: 285 loop : -0.43 (0.28), residues: 453 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 0.017 0.001 PHE A 189 TYR 0.012 0.001 TYR R 313 ARG 0.009 0.000 ARG A 32 *********************** 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 234 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7978 (m-30) cc_final: 0.7628 (m-30) REVERT: A 197 LYS cc_start: 0.8289 (mtpm) cc_final: 0.7960 (mtpp) REVERT: A 243 MET cc_start: 0.8470 (tpp) cc_final: 0.8228 (tpp) REVERT: A 245 GLU cc_start: 0.7333 (tp30) cc_final: 0.7058 (tp30) REVERT: A 260 THR cc_start: 0.8651 (m) cc_final: 0.8393 (p) REVERT: A 324 THR cc_start: 0.7583 (m) cc_final: 0.6988 (p) REVERT: B 150 ARG cc_start: 0.8854 (mmt-90) cc_final: 0.8565 (mpt180) REVERT: N 142 GLN cc_start: 0.8650 (mt0) cc_final: 0.8439 (mt0) REVERT: N 202 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8088 (ttp-170) REVERT: R 82 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8033 (mm) REVERT: R 124 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7357 (mm-30) REVERT: R 142 TYR cc_start: 0.8527 (t80) cc_final: 0.8309 (t80) REVERT: R 150 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7868 (ttm170) REVERT: R 237 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7592 (ttp80) REVERT: R 283 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7158 (mtt180) REVERT: R 332 VAL cc_start: 0.8533 (p) cc_final: 0.8285 (m) outliers start: 33 outliers final: 21 residues processed: 216 average time/residue: 1.2107 time to fit residues: 279.2384 Evaluate side-chains 225 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 44 GLN 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 12 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 82 LEU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 149 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 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: 1.9990 chunk 108 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 24 optimal weight: 0.0020 chunk 105 optimal weight: 0.8980 chunk 95 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.2386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112120 restraints weight = 12491.457| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.52 r_work: 0.3384 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9233 Z= 0.156 Angle : 0.721 30.792 12507 Z= 0.319 Chirality : 0.062 1.769 1418 Planarity : 0.004 0.061 1566 Dihedral : 11.742 178.157 1375 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.16 % Allowed : 18.96 % Favored : 77.88 % 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: 0.74 (0.25), residues: 1119 helix: 1.66 (0.27), residues: 379 sheet: 0.35 (0.29), residues: 290 loop : -0.34 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS B 142 PHE 0.016 0.001 PHE R 309 TYR 0.012 0.001 TYR N 190 ARG 0.010 0.000 ARG A 32 *********************** 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 235 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8014 (m-30) cc_final: 0.7649 (m-30) REVERT: A 243 MET cc_start: 0.8446 (tpp) cc_final: 0.8214 (tpp) REVERT: A 245 GLU cc_start: 0.7312 (tp30) cc_final: 0.7014 (tp30) REVERT: A 260 THR cc_start: 0.8665 (m) cc_final: 0.8387 (p) REVERT: A 324 THR cc_start: 0.7453 (m) cc_final: 0.6862 (p) REVERT: B 150 ARG cc_start: 0.8838 (mmt-90) cc_final: 0.8570 (mpt180) REVERT: B 215 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6715 (pp20) REVERT: N 202 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8025 (ttp-170) REVERT: R 82 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8019 (mm) REVERT: R 142 TYR cc_start: 0.8525 (t80) cc_final: 0.8309 (t80) REVERT: R 150 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7810 (ttm170) REVERT: R 237 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7605 (ttp80) REVERT: R 283 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7296 (mtt180) REVERT: R 332 VAL cc_start: 0.8540 (p) cc_final: 0.8286 (m) outliers start: 31 outliers final: 18 residues processed: 218 average time/residue: 1.2280 time to fit residues: 285.4771 Evaluate side-chains 225 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 82 LEU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain L residue 10 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 0.7980 chunk 95 optimal weight: 0.0970 chunk 24 optimal weight: 0.0870 chunk 110 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 0.0170 chunk 7 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 44 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112335 restraints weight = 12366.027| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.50 r_work: 0.3384 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9233 Z= 0.163 Angle : 0.712 30.768 12507 Z= 0.315 Chirality : 0.062 1.767 1418 Planarity : 0.004 0.063 1566 Dihedral : 11.709 178.757 1375 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.85 % Allowed : 19.06 % Favored : 78.08 % 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: 0.79 (0.25), residues: 1119 helix: 1.79 (0.27), residues: 373 sheet: 0.35 (0.28), residues: 288 loop : -0.35 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS B 142 PHE 0.016 0.001 PHE R 309 TYR 0.011 0.001 TYR N 190 ARG 0.010 0.000 ARG A 32 *********************** 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 226 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8025 (m-30) cc_final: 0.7659 (m-30) REVERT: A 243 MET cc_start: 0.8453 (tpp) cc_final: 0.8221 (tpp) REVERT: A 245 GLU cc_start: 0.7301 (tp30) cc_final: 0.7044 (tp30) REVERT: A 324 THR cc_start: 0.7489 (m) cc_final: 0.6882 (p) REVERT: B 87 THR cc_start: 0.8314 (p) cc_final: 0.8114 (m) REVERT: B 150 ARG cc_start: 0.8824 (mmt-90) cc_final: 0.8559 (mpt180) REVERT: B 215 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6728 (pp20) REVERT: N 202 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8016 (ttp-170) REVERT: R 82 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7998 (mm) REVERT: R 150 ARG cc_start: 0.8042 (ttm110) cc_final: 0.7793 (ttm170) REVERT: R 237 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7528 (ttp80) REVERT: R 332 VAL cc_start: 0.8539 (p) cc_final: 0.8290 (m) outliers start: 28 outliers final: 16 residues processed: 213 average time/residue: 1.2376 time to fit residues: 281.0221 Evaluate side-chains 216 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL 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 82 LEU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain L residue 10 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 142 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 = 0.3641 r_free = 0.3641 target = 0.122873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110359 restraints weight = 12431.889| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.51 r_work: 0.3364 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9233 Z= 0.261 Angle : 0.755 30.764 12507 Z= 0.339 Chirality : 0.064 1.765 1418 Planarity : 0.004 0.064 1566 Dihedral : 11.813 179.007 1375 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.65 % Allowed : 19.78 % Favored : 77.57 % 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: 0.65 (0.25), residues: 1119 helix: 1.61 (0.27), residues: 379 sheet: 0.21 (0.28), residues: 290 loop : -0.34 (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 N 35 PHE 0.019 0.002 PHE A 189 TYR 0.014 0.001 TYR R 313 ARG 0.011 0.000 ARG A 32 ********************** 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 225 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7998 (m-30) cc_final: 0.7647 (m-30) REVERT: A 243 MET cc_start: 0.8443 (tpp) cc_final: 0.8209 (tpp) REVERT: A 245 GLU cc_start: 0.7288 (tp30) cc_final: 0.7033 (tp30) REVERT: A 324 THR cc_start: 0.7607 (m) cc_final: 0.6990 (p) REVERT: B 22 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7627 (mtp180) REVERT: B 215 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6757 (pp20) REVERT: N 202 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8045 (ttp-170) REVERT: R 82 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8026 (mm) REVERT: R 237 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7523 (ttp80) REVERT: R 332 VAL cc_start: 0.8539 (p) cc_final: 0.8299 (m) outliers start: 26 outliers final: 16 residues processed: 210 average time/residue: 1.1976 time to fit residues: 269.2316 Evaluate side-chains 217 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 82 LEU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain L residue 10 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.123041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110555 restraints weight = 12379.065| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.50 r_work: 0.3366 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9233 Z= 0.247 Angle : 0.747 30.757 12507 Z= 0.336 Chirality : 0.063 1.768 1418 Planarity : 0.004 0.063 1566 Dihedral : 11.801 179.244 1375 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.45 % Allowed : 20.18 % Favored : 77.37 % 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: 0.65 (0.25), residues: 1119 helix: 1.60 (0.27), residues: 379 sheet: 0.26 (0.29), residues: 284 loop : -0.37 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.001 PHE A 189 TYR 0.012 0.001 TYR R 313 ARG 0.011 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7654.71 seconds wall clock time: 136 minutes 10.22 seconds (8170.22 seconds total)