Starting phenix.real_space_refine on Fri Nov 15 09:00:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjd_60141/11_2024/8zjd_60141.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjd_60141/11_2024/8zjd_60141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjd_60141/11_2024/8zjd_60141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjd_60141/11_2024/8zjd_60141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjd_60141/11_2024/8zjd_60141.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zjd_60141/11_2024/8zjd_60141.cif" } resolution = 3.06 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= 0.007 sd= 0.058 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 55 5.16 5 C 5617 2.51 5 N 1521 2.21 5 O 1627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8820 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2204 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 268} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2555 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "S" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1741 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 386 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 50} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1840 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 5.15, per 1000 atoms: 0.58 Number of scatterers: 8820 At special positions: 0 Unit cell: (97.09, 115.34, 129.21, 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 55 16.00 O 1627 8.00 N 1521 7.00 C 5617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 191 " distance=2.33 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: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 40.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'R' and resid 43 through 69 removed outlier: 3.823A pdb=" N LEU R 47 " --> pdb=" O TRP R 43 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 94 Processing helix chain 'R' and resid 95 through 103 removed outlier: 3.624A pdb=" N ALA R 100 " --> pdb=" O VAL R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 Processing helix chain 'R' and resid 148 through 152 removed outlier: 3.571A pdb=" N HIS R 152 " --> pdb=" O ARG R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 Processing helix chain 'R' and resid 175 through 180 removed outlier: 4.307A pdb=" N ALA R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 213 Processing helix chain 'R' and resid 213 through 234 Processing helix chain 'R' and resid 244 through 289 removed outlier: 5.285A pdb=" N ALA R 256 " --> pdb=" O GLU R 252 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL R 257 " --> pdb=" O ARG R 253 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 298 through 324 removed outlier: 3.729A pdb=" N SER R 316 " --> pdb=" O SER R 312 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'R' and resid 327 through 337 Processing helix chain 'L' and resid 212 through 216 Processing helix chain 'B' and resid 10 through 31 removed outlier: 4.435A pdb=" N GLN B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.781A pdb=" N ILE B 275 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 31 Processing helix chain 'S' and resid 52 through 55 Processing helix chain 'S' and resid 61 through 64 removed outlier: 3.588A pdb=" N LYS S 64 " --> pdb=" O ASP S 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 61 through 64' Processing helix chain 'S' and resid 73 through 75 No H-bonds generated for 'chain 'S' and resid 73 through 75' Processing helix chain 'S' and resid 86 through 90 Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.580A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.603A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.427A pdb=" N ILE A 219 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N HIS A 220 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 337 through 358 Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 184 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57 removed outlier: 4.171A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 336 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS B 322 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.763A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.787A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 4.388A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.798A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 213 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR B 226 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 215 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 222 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.620A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 282 through 283 removed outlier: 3.781A pdb=" N CYS B 299 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 2 through 5 removed outlier: 5.411A pdb=" N GLY S 15 " --> pdb=" O SER S 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 9 through 11 removed outlier: 6.951A pdb=" N MET S 33 " --> pdb=" O TYR S 49 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR S 49 " --> pdb=" O MET S 33 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP S 35 " --> pdb=" O VAL S 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.714A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 192 through 197 removed outlier: 9.849A pdb=" N SER A 227 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS A 35 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N MET A 229 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 37 " --> pdb=" O MET A 229 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU A 231 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 39 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ALA A 233 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 228 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE A 274 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE A 230 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN A 276 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 232 " --> pdb=" O ASN A 276 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1308 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: 2.55 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1432 1.31 - 1.44: 2527 1.44 - 1.56: 4973 1.56 - 1.69: 1 1.69 - 1.82: 79 Bond restraints: 9012 Sorted by residual: bond pdb=" CA VAL R 138 " pdb=" C VAL R 138 " ideal model delta sigma weight residual 1.525 1.465 0.060 1.27e-02 6.20e+03 2.25e+01 bond pdb=" C ASP R 139 " pdb=" O ASP R 139 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.19e-02 7.06e+03 1.61e+01 bond pdb=" CA LYS A 356 " pdb=" C LYS A 356 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" C ARG R 140 " pdb=" O ARG R 140 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.25e-02 6.40e+03 1.48e+01 bond pdb=" CA ASP R 139 " pdb=" C ASP R 139 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.29e-02 6.01e+03 1.46e+01 ... (remaining 9007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11956 1.92 - 3.83: 246 3.83 - 5.75: 32 5.75 - 7.67: 5 7.67 - 9.59: 5 Bond angle restraints: 12244 Sorted by residual: angle pdb=" N ASP B 81 " pdb=" CA ASP B 81 " pdb=" C ASP B 81 " ideal model delta sigma weight residual 113.16 103.83 9.33 1.24e+00 6.50e-01 5.67e+01 angle pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" C TYR A 358 " ideal model delta sigma weight residual 112.97 106.95 6.02 1.06e+00 8.90e-01 3.22e+01 angle pdb=" N VAL R 249 " pdb=" CA VAL R 249 " pdb=" C VAL R 249 " ideal model delta sigma weight residual 110.74 105.63 5.11 9.10e-01 1.21e+00 3.15e+01 angle pdb=" N VAL R 138 " pdb=" CA VAL R 138 " pdb=" C VAL R 138 " ideal model delta sigma weight residual 113.16 106.38 6.78 1.49e+00 4.50e-01 2.07e+01 angle pdb=" N ASP R 139 " pdb=" CA ASP R 139 " pdb=" C ASP R 139 " ideal model delta sigma weight residual 111.40 105.88 5.52 1.22e+00 6.72e-01 2.05e+01 ... (remaining 12239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4796 17.79 - 35.57: 397 35.57 - 53.36: 100 53.36 - 71.15: 14 71.15 - 88.94: 10 Dihedral angle restraints: 5317 sinusoidal: 1999 harmonic: 3318 Sorted by residual: dihedral pdb=" CB CYS R 115 " pdb=" SG CYS R 115 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual 93.00 4.06 88.94 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CA GLN S 12 " pdb=" C GLN S 12 " pdb=" N PRO S 13 " pdb=" CA PRO S 13 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS B 83 " pdb=" C LYS B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1300 0.091 - 0.182: 84 0.182 - 0.272: 6 0.272 - 0.363: 2 0.363 - 0.454: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ASN A 359 " pdb=" N ASN A 359 " pdb=" C ASN A 359 " pdb=" CB ASN A 359 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA VAL R 249 " pdb=" N VAL R 249 " pdb=" C VAL R 249 " pdb=" CB VAL R 249 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA LEU R 245 " pdb=" N LEU R 245 " pdb=" C LEU R 245 " pdb=" CB LEU R 245 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1390 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 136 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C MET R 136 " 0.037 2.00e-02 2.50e+03 pdb=" O MET R 136 " -0.013 2.00e-02 2.50e+03 pdb=" N SER R 137 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 256 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C ALA R 256 " -0.036 2.00e-02 2.50e+03 pdb=" O ALA R 256 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL R 257 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 338 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ASP B 338 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP B 338 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 339 " -0.011 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 839 2.74 - 3.28: 9025 3.28 - 3.82: 14756 3.82 - 4.36: 17644 4.36 - 4.90: 31154 Nonbonded interactions: 73418 Sorted by model distance: nonbonded pdb=" OH TYR A 237 " pdb=" OG SER A 288 " model vdw 2.200 3.040 nonbonded pdb=" O ARG R 297 " pdb=" OH TYR L 211 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 150 " pdb=" OD2 ASP B 191 " model vdw 2.302 3.040 nonbonded pdb=" O VAL R 96 " pdb=" OG1 THR R 99 " model vdw 2.308 3.040 nonbonded pdb=" O ASP B 210 " pdb=" OD1 ASP B 210 " model vdw 2.322 3.040 ... (remaining 73413 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: 1.080 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.400 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9012 Z= 0.284 Angle : 0.674 9.587 12244 Z= 0.398 Chirality : 0.046 0.454 1393 Planarity : 0.004 0.050 1557 Dihedral : 14.501 85.750 3172 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.54 % Allowed : 14.67 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1121 helix: 1.57 (0.26), residues: 417 sheet: 0.27 (0.32), residues: 278 loop : -0.34 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.002 0.001 HIS B 147 PHE 0.016 0.001 PHE L 220 TYR 0.015 0.001 TYR R 65 ARG 0.010 0.000 ARG L 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 1.126 Fit side-chains REVERT: R 62 LEU cc_start: 0.8167 (mp) cc_final: 0.7961 (mp) REVERT: R 71 LYS cc_start: 0.6979 (mmmt) cc_final: 0.6734 (tptp) REVERT: R 78 ASN cc_start: 0.8894 (m110) cc_final: 0.8665 (m110) REVERT: R 253 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6590 (ttp-170) REVERT: R 315 ASN cc_start: 0.8264 (t0) cc_final: 0.8042 (t0) REVERT: B 222 MET cc_start: 0.7156 (ptt) cc_final: 0.6885 (ptm) REVERT: B 273 ASN cc_start: 0.8509 (m110) cc_final: 0.8171 (m110) REVERT: S 45 GLU cc_start: 0.7652 (tt0) cc_final: 0.7443 (tt0) REVERT: G 31 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8693 (tptt) REVERT: G 46 GLU cc_start: 0.8252 (mp0) cc_final: 0.7867 (mp0) outliers start: 5 outliers final: 3 residues processed: 160 average time/residue: 0.2502 time to fit residues: 53.3704 Evaluate side-chains 130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 CYS Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN R 83 ASN B 273 ASN S 38 GLN S 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9012 Z= 0.288 Angle : 0.612 6.732 12244 Z= 0.323 Chirality : 0.044 0.156 1393 Planarity : 0.004 0.052 1557 Dihedral : 5.381 57.918 1250 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.27 % Allowed : 15.10 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1121 helix: 1.78 (0.25), residues: 409 sheet: 0.24 (0.31), residues: 285 loop : -0.40 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.004 0.001 HIS B 147 PHE 0.012 0.001 PHE S 28 TYR 0.015 0.002 TYR B 64 ARG 0.005 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.958 Fit side-chains REVERT: R 71 LYS cc_start: 0.7028 (mmmt) cc_final: 0.6769 (tptp) REVERT: R 212 LEU cc_start: 0.8342 (mp) cc_final: 0.8081 (mp) REVERT: R 253 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6491 (ttp-170) REVERT: R 305 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8227 (tmtt) REVERT: B 134 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7715 (ttt90) REVERT: B 135 GLU cc_start: 0.8632 (mp0) cc_final: 0.8328 (mp0) REVERT: B 222 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6866 (ptm) REVERT: B 273 ASN cc_start: 0.8571 (m-40) cc_final: 0.8249 (m110) REVERT: S 81 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7569 (tp-100) REVERT: G 31 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8617 (tptt) REVERT: G 46 GLU cc_start: 0.8280 (mp0) cc_final: 0.7969 (mp0) outliers start: 21 outliers final: 10 residues processed: 150 average time/residue: 0.2231 time to fit residues: 45.9938 Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain L residue 214 ASN Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.0870 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 ASN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN S 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9012 Z= 0.264 Angle : 0.570 5.926 12244 Z= 0.299 Chirality : 0.043 0.160 1393 Planarity : 0.004 0.048 1557 Dihedral : 5.224 53.246 1249 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.24 % Allowed : 14.56 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1121 helix: 1.91 (0.25), residues: 406 sheet: 0.22 (0.32), residues: 275 loop : -0.53 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.003 0.001 HIS S 34 PHE 0.011 0.001 PHE B 246 TYR 0.025 0.002 TYR A 237 ARG 0.004 0.000 ARG S 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.962 Fit side-chains REVERT: R 71 LYS cc_start: 0.7077 (mmmt) cc_final: 0.6732 (tptp) REVERT: R 212 LEU cc_start: 0.8350 (mp) cc_final: 0.8066 (mp) REVERT: R 253 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6431 (ttp-170) REVERT: B 222 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6931 (ptm) REVERT: B 273 ASN cc_start: 0.8586 (m-40) cc_final: 0.8343 (m110) REVERT: B 274 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7705 (pp) REVERT: S 81 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7478 (tp-100) REVERT: G 46 GLU cc_start: 0.8239 (mp0) cc_final: 0.7999 (mp0) outliers start: 30 outliers final: 16 residues processed: 156 average time/residue: 0.2038 time to fit residues: 44.4060 Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain L residue 214 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 213 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN R 309 HIS B 300 ASN S 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9012 Z= 0.211 Angle : 0.549 6.509 12244 Z= 0.286 Chirality : 0.042 0.140 1393 Planarity : 0.004 0.052 1557 Dihedral : 5.062 48.204 1249 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.59 % Allowed : 16.40 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1121 helix: 1.95 (0.25), residues: 409 sheet: 0.13 (0.32), residues: 277 loop : -0.49 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.003 0.001 HIS S 34 PHE 0.010 0.001 PHE B 246 TYR 0.013 0.001 TYR R 65 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.894 Fit side-chains REVERT: R 71 LYS cc_start: 0.7150 (mmmt) cc_final: 0.6859 (tptp) REVERT: R 160 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7356 (tt) REVERT: R 212 LEU cc_start: 0.8364 (mp) cc_final: 0.8121 (mp) REVERT: R 253 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6402 (ttp-170) REVERT: R 305 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8188 (tmtt) REVERT: R 309 HIS cc_start: 0.8063 (m-70) cc_final: 0.7711 (m-70) REVERT: B 222 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6994 (ptm) REVERT: B 273 ASN cc_start: 0.8590 (m-40) cc_final: 0.8343 (m110) REVERT: S 81 GLN cc_start: 0.7797 (tp-100) cc_final: 0.7456 (tp-100) REVERT: S 86 ARG cc_start: 0.7593 (mtp85) cc_final: 0.6899 (mtt-85) REVERT: G 46 GLU cc_start: 0.8254 (mp0) cc_final: 0.7964 (mp0) outliers start: 24 outliers final: 18 residues processed: 159 average time/residue: 0.2196 time to fit residues: 48.2559 Evaluate side-chains 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain L residue 214 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 314 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 ASN B 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9012 Z= 0.224 Angle : 0.556 8.951 12244 Z= 0.288 Chirality : 0.042 0.142 1393 Planarity : 0.004 0.051 1557 Dihedral : 4.984 47.759 1249 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.59 % Allowed : 17.69 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1121 helix: 2.03 (0.25), residues: 408 sheet: 0.10 (0.32), residues: 277 loop : -0.58 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.003 0.001 HIS R 309 PHE 0.010 0.001 PHE R 282 TYR 0.020 0.001 TYR L 211 ARG 0.006 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.904 Fit side-chains REVERT: R 71 LYS cc_start: 0.7132 (mmmt) cc_final: 0.6794 (tptp) REVERT: R 160 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7360 (tt) REVERT: R 212 LEU cc_start: 0.8491 (mp) cc_final: 0.8253 (mp) REVERT: R 253 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6413 (ttp-170) REVERT: B 222 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7030 (ptm) REVERT: B 273 ASN cc_start: 0.8596 (m-40) cc_final: 0.8332 (m110) REVERT: B 274 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7683 (pp) REVERT: S 66 ARG cc_start: 0.7524 (ttm170) cc_final: 0.7314 (ttp-170) REVERT: S 81 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7409 (tp-100) REVERT: S 86 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7006 (mtt-85) REVERT: G 46 GLU cc_start: 0.8246 (mp0) cc_final: 0.7954 (mp0) outliers start: 24 outliers final: 17 residues processed: 151 average time/residue: 0.2034 time to fit residues: 42.8680 Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain L residue 214 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9012 Z= 0.213 Angle : 0.545 7.731 12244 Z= 0.284 Chirality : 0.042 0.146 1393 Planarity : 0.004 0.053 1557 Dihedral : 4.812 46.544 1247 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.91 % Allowed : 18.23 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1121 helix: 2.07 (0.25), residues: 408 sheet: 0.10 (0.32), residues: 277 loop : -0.63 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.005 0.001 HIS R 181 PHE 0.010 0.001 PHE R 282 TYR 0.016 0.001 TYR B 64 ARG 0.007 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.998 Fit side-chains REVERT: R 71 LYS cc_start: 0.7142 (mmmt) cc_final: 0.6806 (tptp) REVERT: R 160 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7371 (tt) REVERT: R 212 LEU cc_start: 0.8482 (mp) cc_final: 0.8262 (mp) REVERT: R 253 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6352 (ttp-110) REVERT: B 222 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7080 (ptm) REVERT: B 273 ASN cc_start: 0.8606 (m-40) cc_final: 0.8343 (m110) REVERT: B 274 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7641 (pp) REVERT: B 280 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8588 (m) REVERT: S 66 ARG cc_start: 0.7505 (ttm170) cc_final: 0.7295 (ttp-170) REVERT: S 86 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7032 (mtt-85) REVERT: G 46 GLU cc_start: 0.8245 (mp0) cc_final: 0.7945 (mp0) outliers start: 27 outliers final: 18 residues processed: 158 average time/residue: 0.2028 time to fit residues: 45.3956 Evaluate side-chains 152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain L residue 214 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 ASN S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9012 Z= 0.178 Angle : 0.551 8.863 12244 Z= 0.282 Chirality : 0.041 0.154 1393 Planarity : 0.004 0.052 1557 Dihedral : 4.717 46.334 1247 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.70 % Allowed : 19.20 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1121 helix: 2.08 (0.26), residues: 408 sheet: 0.12 (0.32), residues: 266 loop : -0.60 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.004 0.001 HIS R 181 PHE 0.010 0.001 PHE R 282 TYR 0.014 0.001 TYR R 190 ARG 0.006 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.974 Fit side-chains REVERT: R 71 LYS cc_start: 0.7147 (mmmt) cc_final: 0.6808 (tptp) REVERT: R 212 LEU cc_start: 0.8443 (mp) cc_final: 0.8242 (mp) REVERT: R 253 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6322 (ttp-110) REVERT: B 222 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7086 (ptm) REVERT: B 225 GLN cc_start: 0.8326 (mp10) cc_final: 0.8042 (mp10) REVERT: B 273 ASN cc_start: 0.8597 (m-40) cc_final: 0.8338 (m110) REVERT: B 274 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7671 (pp) REVERT: B 280 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8568 (m) REVERT: S 66 ARG cc_start: 0.7484 (ttm170) cc_final: 0.7225 (ttm170) REVERT: S 86 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7029 (mtt-85) outliers start: 25 outliers final: 17 residues processed: 160 average time/residue: 0.2027 time to fit residues: 45.7000 Evaluate side-chains 154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain L residue 214 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain S residue 54 SER Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9012 Z= 0.145 Angle : 0.533 9.330 12244 Z= 0.272 Chirality : 0.041 0.159 1393 Planarity : 0.004 0.054 1557 Dihedral : 4.525 45.958 1247 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.05 % Allowed : 20.28 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1121 helix: 2.20 (0.26), residues: 408 sheet: 0.19 (0.32), residues: 265 loop : -0.59 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.004 0.001 HIS R 181 PHE 0.008 0.001 PHE B 204 TYR 0.014 0.001 TYR R 190 ARG 0.006 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.974 Fit side-chains REVERT: R 71 LYS cc_start: 0.7103 (mmmt) cc_final: 0.6787 (tptp) REVERT: R 253 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6299 (ttp-110) REVERT: B 222 MET cc_start: 0.7379 (ptt) cc_final: 0.7126 (ptm) REVERT: B 273 ASN cc_start: 0.8573 (m-40) cc_final: 0.8340 (m110) REVERT: B 274 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7644 (pp) REVERT: B 280 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8555 (m) REVERT: S 66 ARG cc_start: 0.7442 (ttm170) cc_final: 0.7186 (ttm170) REVERT: S 86 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7016 (mtt-85) outliers start: 19 outliers final: 14 residues processed: 163 average time/residue: 0.1974 time to fit residues: 45.2067 Evaluate side-chains 157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 0.0570 chunk 43 optimal weight: 0.0970 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.0980 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 ASN R 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9012 Z= 0.135 Angle : 0.547 9.632 12244 Z= 0.275 Chirality : 0.040 0.164 1393 Planarity : 0.004 0.054 1557 Dihedral : 4.397 46.465 1247 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.83 % Allowed : 20.82 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1121 helix: 2.26 (0.26), residues: 408 sheet: 0.25 (0.32), residues: 259 loop : -0.55 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 174 HIS 0.004 0.001 HIS R 181 PHE 0.008 0.001 PHE B 204 TYR 0.014 0.001 TYR R 190 ARG 0.010 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.878 Fit side-chains REVERT: R 71 LYS cc_start: 0.7098 (mmmt) cc_final: 0.6766 (tptp) REVERT: R 253 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6240 (ttp-110) REVERT: B 222 MET cc_start: 0.7377 (ptt) cc_final: 0.7122 (ptm) REVERT: B 225 GLN cc_start: 0.8318 (mp10) cc_final: 0.8080 (mp10) REVERT: B 273 ASN cc_start: 0.8520 (m-40) cc_final: 0.8292 (m110) REVERT: B 274 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7650 (pp) REVERT: B 280 SER cc_start: 0.9036 (OUTLIER) cc_final: 0.8523 (m) REVERT: B 298 ASN cc_start: 0.8390 (m-40) cc_final: 0.7535 (p0) REVERT: B 326 THR cc_start: 0.7847 (p) cc_final: 0.7643 (p) REVERT: S 66 ARG cc_start: 0.7473 (ttm170) cc_final: 0.7254 (ttm170) REVERT: S 86 ARG cc_start: 0.7699 (mtp85) cc_final: 0.7104 (mtt-85) REVERT: S 206 SER cc_start: 0.8447 (p) cc_final: 0.7997 (t) REVERT: A 20 ASP cc_start: 0.8360 (m-30) cc_final: 0.8150 (m-30) outliers start: 17 outliers final: 13 residues processed: 166 average time/residue: 0.1985 time to fit residues: 46.8430 Evaluate side-chains 163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9012 Z= 0.192 Angle : 0.579 10.432 12244 Z= 0.290 Chirality : 0.042 0.167 1393 Planarity : 0.004 0.056 1557 Dihedral : 4.474 46.166 1247 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.94 % Allowed : 21.04 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1121 helix: 2.23 (0.26), residues: 409 sheet: 0.24 (0.32), residues: 265 loop : -0.54 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.004 0.001 HIS R 181 PHE 0.009 0.001 PHE B 246 TYR 0.019 0.001 TYR B 64 ARG 0.007 0.000 ARG A 302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.977 Fit side-chains REVERT: R 71 LYS cc_start: 0.7135 (mmmt) cc_final: 0.6886 (tptp) REVERT: R 253 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6285 (ttp-110) REVERT: B 222 MET cc_start: 0.7364 (ptt) cc_final: 0.7114 (ptm) REVERT: B 225 GLN cc_start: 0.8324 (mp10) cc_final: 0.8059 (mp10) REVERT: B 273 ASN cc_start: 0.8560 (m-40) cc_final: 0.8324 (m110) REVERT: B 274 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7662 (pp) REVERT: B 280 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8574 (m) REVERT: B 298 ASN cc_start: 0.8498 (m-40) cc_final: 0.7572 (p0) REVERT: S 66 ARG cc_start: 0.7449 (ttm170) cc_final: 0.7197 (ttm170) REVERT: S 86 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7100 (mtt-85) REVERT: S 92 MET cc_start: 0.8542 (ttm) cc_final: 0.7450 (tpp) REVERT: S 206 SER cc_start: 0.8468 (p) cc_final: 0.7984 (t) REVERT: A 262 THR cc_start: 0.8504 (m) cc_final: 0.8064 (p) outliers start: 18 outliers final: 15 residues processed: 157 average time/residue: 0.2053 time to fit residues: 45.0093 Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.0040 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 ASN R 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.153834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112244 restraints weight = 12590.078| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.88 r_work: 0.3267 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9012 Z= 0.204 Angle : 0.578 10.343 12244 Z= 0.291 Chirality : 0.042 0.161 1393 Planarity : 0.004 0.053 1557 Dihedral : 4.543 44.855 1247 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.27 % Allowed : 20.82 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1121 helix: 2.23 (0.26), residues: 409 sheet: 0.25 (0.33), residues: 261 loop : -0.47 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.004 0.001 HIS R 181 PHE 0.009 0.001 PHE B 246 TYR 0.023 0.001 TYR B 64 ARG 0.007 0.000 ARG A 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.94 seconds wall clock time: 40 minutes 25.63 seconds (2425.63 seconds total)