Starting phenix.real_space_refine on Sun Aug 4 06:32:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vug_32127/08_2024/7vug_32127.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vug_32127/08_2024/7vug_32127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vug_32127/08_2024/7vug_32127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vug_32127/08_2024/7vug_32127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vug_32127/08_2024/7vug_32127.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vug_32127/08_2024/7vug_32127.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1050 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 61 5.16 5 Cl 1 4.86 5 C 5711 2.51 5 N 1503 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8924 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 2313 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} Conformer: "B" Number of residues, atoms: 282, 2313 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} bond proxies already assigned to first conformer: 2369 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7ZQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.35, per 1000 atoms: 0.71 Number of scatterers: 8924 At special positions: 0 Unit cell: (88.4, 121.68, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 61 16.00 O 1648 8.00 N 1503 7.00 C 5711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.65 Conformation dependent library (CDL) restraints added in 1.9 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 16 sheets defined 38.2% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 44 through 54 removed outlier: 3.617A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.380A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.080A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.578A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 25 No H-bonds generated for 'chain 'R' and resid 23 through 25' Processing helix chain 'R' and resid 26 through 52 removed outlier: 4.209A pdb=" N VAL R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL R 31 " --> pdb=" O PHE R 27 " (cutoff:3.500A) Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 53 through 58 Processing helix chain 'R' and resid 60 through 81 removed outlier: 3.697A pdb=" N ASN R 64 " --> pdb=" O LYS R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 88 Processing helix chain 'R' and resid 99 through 132 removed outlier: 3.808A pdb=" N THR R 119 " --> pdb=" O SER R 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL R 120 " --> pdb=" O ILE R 116 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 135 through 140 Processing helix chain 'R' and resid 141 through 160 removed outlier: 3.592A pdb=" N LYS R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 166 removed outlier: 3.714A pdb=" N TRP R 165 " --> pdb=" O PRO R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 192 Processing helix chain 'R' and resid 192 through 212 Processing helix chain 'R' and resid 220 through 242 removed outlier: 3.842A pdb=" N ILE R 236 " --> pdb=" O THR R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 254 removed outlier: 4.229A pdb=" N ILE R 248 " --> pdb=" O ARG R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 287 removed outlier: 3.523A pdb=" N VAL R 263 " --> pdb=" O ASN R 259 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE R 282 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 304 Processing helix chain 'S' and resid 52 through 56 removed outlier: 4.044A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.355A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 50 removed outlier: 5.716A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.803A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 83 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.736A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.610A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.232A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.892A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.267A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.591A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.591A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'S' and resid 45 through 51 removed outlier: 6.584A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.699A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 147 Processing sheet with id=AB7, first strand: chain 'S' and resid 165 through 167 405 hydrogen bonds defined for protein. 1143 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: 2.50 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1426 1.31 - 1.43: 2494 1.43 - 1.56: 5115 1.56 - 1.68: 0 1.68 - 1.81: 89 Bond restraints: 9124 Sorted by residual: bond pdb=" C9 7ZQ R 401 " pdb=" N2 7ZQ R 401 " ideal model delta sigma weight residual 1.341 1.444 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C7 7ZQ R 401 " pdb=" N1 7ZQ R 401 " ideal model delta sigma weight residual 1.344 1.444 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.16e+00 bond pdb=" C3 7ZQ R 401 " pdb="CL1 7ZQ R 401 " ideal model delta sigma weight residual 1.732 1.784 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" N LYS A 277 " pdb=" CA LYS A 277 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.37e+00 ... (remaining 9119 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.63: 136 105.63 - 112.71: 4849 112.71 - 119.80: 2972 119.80 - 126.88: 4292 126.88 - 133.96: 120 Bond angle restraints: 12369 Sorted by residual: angle pdb=" CA ILE A 278 " pdb=" C ILE A 278 " pdb=" O ILE A 278 " ideal model delta sigma weight residual 121.17 118.05 3.12 1.06e+00 8.90e-01 8.67e+00 angle pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " pdb=" CG TYR S 223 " ideal model delta sigma weight residual 113.90 108.64 5.26 1.80e+00 3.09e-01 8.54e+00 angle pdb=" C GLU A 275 " pdb=" N GLU A 276 " pdb=" CA GLU A 276 " ideal model delta sigma weight residual 120.44 123.99 -3.55 1.36e+00 5.41e-01 6.81e+00 angle pdb=" CA LYS R 301 " pdb=" C LYS R 301 " pdb=" O LYS R 301 " ideal model delta sigma weight residual 121.00 118.26 2.74 1.05e+00 9.07e-01 6.80e+00 angle pdb=" CA LYS A 279 " pdb=" C LYS A 279 " pdb=" O LYS A 279 " ideal model delta sigma weight residual 120.82 118.16 2.66 1.05e+00 9.07e-01 6.41e+00 ... (remaining 12364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4864 17.41 - 34.83: 441 34.83 - 52.24: 74 52.24 - 69.65: 14 69.65 - 87.06: 3 Dihedral angle restraints: 5396 sinusoidal: 2107 harmonic: 3289 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 146.54 -53.54 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CA ASN R 93 " pdb=" C ASN R 93 " pdb=" N MET R 94 " pdb=" CA MET R 94 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA GLU S 222 " pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 5393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 899 0.034 - 0.068: 344 0.068 - 0.103: 111 0.103 - 0.137: 38 0.137 - 0.171: 10 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CG LEU S 4 " pdb=" CB LEU S 4 " pdb=" CD1 LEU S 4 " pdb=" CD2 LEU S 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 1399 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP R 166 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO R 167 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 167 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 167 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO S 224 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 84 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C ASP R 84 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP R 84 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE R 85 " 0.012 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 164 2.66 - 3.22: 8576 3.22 - 3.78: 14085 3.78 - 4.34: 18997 4.34 - 4.90: 31814 Nonbonded interactions: 73636 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.099 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.199 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.221 3.040 nonbonded pdb=" NH2 ARG R 244 " pdb=" O2 7ZQ R 401 " model vdw 2.223 3.120 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.228 3.120 ... (remaining 73631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.720 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 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 0.103 9124 Z= 0.268 Angle : 0.608 6.003 12369 Z= 0.331 Chirality : 0.043 0.171 1402 Planarity : 0.005 0.063 1552 Dihedral : 13.558 87.063 3271 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -0.75 (0.26), residues: 1112 helix: 1.16 (0.28), residues: 388 sheet: -1.25 (0.31), residues: 280 loop : -1.42 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 241 HIS 0.006 0.001 HIS S 220 PHE 0.022 0.001 PHE A 196 TYR 0.022 0.002 TYR S 223 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.965 Fit side-chains REVERT: A 29 LYS cc_start: 0.7742 (mmpt) cc_final: 0.7473 (mmpt) REVERT: A 209 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7695 (mtmt) REVERT: B 213 VAL cc_start: 0.7793 (m) cc_final: 0.7230 (t) REVERT: R 32 TYR cc_start: 0.7288 (t80) cc_final: 0.6983 (t80) REVERT: R 116 ILE cc_start: 0.7860 (tp) cc_final: 0.7637 (tp) REVERT: R 153 TYR cc_start: 0.7838 (m-80) cc_final: 0.7446 (m-80) REVERT: R 200 PHE cc_start: 0.7065 (m-10) cc_final: 0.6686 (m-80) REVERT: R 205 ILE cc_start: 0.8009 (tp) cc_final: 0.7780 (tp) REVERT: R 266 MET cc_start: 0.6197 (ppp) cc_final: 0.5994 (ppp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2421 time to fit residues: 64.7273 Evaluate side-chains 187 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 220 GLN B 230 ASN B 259 GLN B 268 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9124 Z= 0.269 Angle : 0.620 7.390 12369 Z= 0.328 Chirality : 0.044 0.201 1402 Planarity : 0.005 0.063 1552 Dihedral : 5.297 53.533 1238 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.72 % Allowed : 10.55 % Favored : 88.73 % 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: -0.77 (0.26), residues: 1112 helix: 1.10 (0.27), residues: 391 sheet: -1.27 (0.30), residues: 278 loop : -1.38 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 241 HIS 0.005 0.001 HIS A 188 PHE 0.013 0.001 PHE R 303 TYR 0.024 0.002 TYR S 223 ARG 0.008 0.000 ARG R 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 208 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: B 196 THR cc_start: 0.7694 (m) cc_final: 0.7487 (m) REVERT: B 205 ASP cc_start: 0.6673 (p0) cc_final: 0.6464 (p0) REVERT: B 213 VAL cc_start: 0.7808 (m) cc_final: 0.7401 (t) REVERT: R 32 TYR cc_start: 0.7424 (t80) cc_final: 0.7127 (t80) REVERT: R 116 ILE cc_start: 0.7841 (tp) cc_final: 0.7578 (tp) REVERT: R 205 ILE cc_start: 0.7997 (tp) cc_final: 0.7775 (tp) REVERT: R 236 ILE cc_start: 0.7318 (tp) cc_final: 0.6905 (tp) REVERT: R 266 MET cc_start: 0.6030 (ppp) cc_final: 0.5312 (ppp) REVERT: S 37 VAL cc_start: 0.8307 (m) cc_final: 0.7969 (t) REVERT: S 60 TYR cc_start: 0.7076 (m-80) cc_final: 0.6631 (m-80) REVERT: S 82 GLN cc_start: 0.7517 (tp40) cc_final: 0.7312 (tp40) REVERT: S 130 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6810 (mt0) REVERT: S 143 VAL cc_start: 0.8110 (m) cc_final: 0.7856 (p) outliers start: 7 outliers final: 3 residues processed: 210 average time/residue: 0.2542 time to fit residues: 70.1345 Evaluate side-chains 207 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 203 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 130 GLN Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 340 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9124 Z= 0.271 Angle : 0.602 7.630 12369 Z= 0.316 Chirality : 0.043 0.203 1402 Planarity : 0.005 0.063 1552 Dihedral : 5.364 55.940 1238 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.15 % Allowed : 12.19 % Favored : 85.66 % 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: -0.78 (0.26), residues: 1112 helix: 1.02 (0.27), residues: 394 sheet: -1.41 (0.29), residues: 288 loop : -1.22 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 241 HIS 0.005 0.001 HIS S 220 PHE 0.014 0.001 PHE S 108 TYR 0.027 0.002 TYR S 223 ARG 0.009 0.000 ARG R 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 206 time to evaluate : 0.914 Fit side-chains REVERT: A 29 LYS cc_start: 0.7606 (mmpt) cc_final: 0.7347 (mmpt) REVERT: A 32 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.7959 (mtt-85) REVERT: B 133 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.8041 (m) REVERT: B 147 SER cc_start: 0.8044 (m) cc_final: 0.7787 (p) REVERT: B 205 ASP cc_start: 0.6681 (p0) cc_final: 0.6467 (p0) REVERT: B 213 VAL cc_start: 0.7780 (m) cc_final: 0.7457 (t) REVERT: B 247 ASP cc_start: 0.6341 (t0) cc_final: 0.6099 (t0) REVERT: R 78 PHE cc_start: 0.7482 (t80) cc_final: 0.7206 (t80) REVERT: R 116 ILE cc_start: 0.7855 (tp) cc_final: 0.7607 (tp) REVERT: R 205 ILE cc_start: 0.8009 (tp) cc_final: 0.7799 (tp) REVERT: R 236 ILE cc_start: 0.7365 (tp) cc_final: 0.7001 (tp) REVERT: S 35 HIS cc_start: 0.8391 (m-70) cc_final: 0.8136 (m-70) REVERT: S 37 VAL cc_start: 0.8345 (m) cc_final: 0.7995 (t) REVERT: S 82 GLN cc_start: 0.7506 (tp40) cc_final: 0.7258 (tp40) outliers start: 21 outliers final: 11 residues processed: 213 average time/residue: 0.2435 time to fit residues: 68.3748 Evaluate side-chains 212 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9124 Z= 0.242 Angle : 0.591 7.645 12369 Z= 0.309 Chirality : 0.042 0.201 1402 Planarity : 0.005 0.062 1552 Dihedral : 5.306 56.910 1238 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.95 % Allowed : 14.24 % Favored : 83.81 % 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: -0.69 (0.26), residues: 1112 helix: 1.05 (0.26), residues: 394 sheet: -1.33 (0.30), residues: 285 loop : -1.13 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS S 35 PHE 0.011 0.001 PHE S 108 TYR 0.027 0.002 TYR S 223 ARG 0.007 0.000 ARG R 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 0.977 Fit side-chains REVERT: A 29 LYS cc_start: 0.7623 (mmpt) cc_final: 0.7356 (mmpt) REVERT: A 32 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7940 (mtt-85) REVERT: B 133 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8057 (m) REVERT: B 147 SER cc_start: 0.8050 (m) cc_final: 0.7804 (p) REVERT: B 205 ASP cc_start: 0.6668 (p0) cc_final: 0.6442 (p0) REVERT: B 213 VAL cc_start: 0.7784 (m) cc_final: 0.7449 (t) REVERT: B 247 ASP cc_start: 0.6429 (t0) cc_final: 0.6215 (t0) REVERT: B 254 ASP cc_start: 0.6286 (t0) cc_final: 0.6012 (t0) REVERT: R 78 PHE cc_start: 0.7484 (t80) cc_final: 0.7276 (t80) REVERT: R 116 ILE cc_start: 0.7843 (tp) cc_final: 0.7590 (tp) REVERT: R 205 ILE cc_start: 0.7992 (tp) cc_final: 0.7767 (tp) REVERT: R 236 ILE cc_start: 0.7360 (tp) cc_final: 0.6968 (tp) REVERT: S 82 GLN cc_start: 0.7493 (tp40) cc_final: 0.7257 (tp40) outliers start: 19 outliers final: 14 residues processed: 214 average time/residue: 0.2439 time to fit residues: 68.6064 Evaluate side-chains 218 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 203 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 259 GLN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 9124 Z= 0.413 Angle : 0.660 7.814 12369 Z= 0.349 Chirality : 0.045 0.236 1402 Planarity : 0.005 0.064 1552 Dihedral : 5.658 56.536 1238 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.87 % Allowed : 14.55 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1112 helix: 0.84 (0.26), residues: 391 sheet: -1.26 (0.30), residues: 282 loop : -1.24 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 47 HIS 0.008 0.002 HIS S 35 PHE 0.023 0.002 PHE S 108 TYR 0.034 0.002 TYR S 223 ARG 0.010 0.001 ARG R 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 0.996 Fit side-chains REVERT: A 20 ASP cc_start: 0.7012 (m-30) cc_final: 0.6794 (m-30) REVERT: A 29 LYS cc_start: 0.7706 (mmpt) cc_final: 0.7435 (mmpt) REVERT: A 32 ARG cc_start: 0.8239 (mtt-85) cc_final: 0.8008 (mtt-85) REVERT: B 133 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8108 (m) REVERT: B 147 SER cc_start: 0.8068 (m) cc_final: 0.7806 (p) REVERT: B 173 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7865 (p) REVERT: B 213 VAL cc_start: 0.7825 (m) cc_final: 0.7532 (t) REVERT: B 228 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7083 (p0) REVERT: B 233 CYS cc_start: 0.6917 (t) cc_final: 0.6630 (t) REVERT: B 247 ASP cc_start: 0.6559 (t0) cc_final: 0.6332 (t0) REVERT: B 254 ASP cc_start: 0.6397 (t0) cc_final: 0.6138 (t0) REVERT: B 329 THR cc_start: 0.8029 (t) cc_final: 0.7798 (t) REVERT: R 116 ILE cc_start: 0.7921 (tp) cc_final: 0.7491 (tp) REVERT: R 141 TYR cc_start: 0.7882 (p90) cc_final: 0.7679 (p90) REVERT: R 236 ILE cc_start: 0.7539 (tp) cc_final: 0.7203 (tp) REVERT: R 272 MET cc_start: 0.7504 (mtp) cc_final: 0.7256 (mtp) outliers start: 28 outliers final: 20 residues processed: 220 average time/residue: 0.2377 time to fit residues: 69.4749 Evaluate side-chains 225 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9124 Z= 0.271 Angle : 0.603 7.305 12369 Z= 0.318 Chirality : 0.042 0.220 1402 Planarity : 0.005 0.064 1552 Dihedral : 5.496 57.488 1238 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.97 % Allowed : 16.60 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1112 helix: 0.89 (0.26), residues: 394 sheet: -1.30 (0.30), residues: 281 loop : -1.14 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 111 HIS 0.006 0.001 HIS S 35 PHE 0.011 0.001 PHE R 90 TYR 0.032 0.002 TYR S 223 ARG 0.010 0.000 ARG R 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 201 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.6949 (m-30) cc_final: 0.6733 (m-30) REVERT: B 133 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8104 (m) REVERT: B 147 SER cc_start: 0.8054 (m) cc_final: 0.7814 (p) REVERT: B 173 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7823 (p) REVERT: B 195 ASP cc_start: 0.7254 (t0) cc_final: 0.7041 (t0) REVERT: B 205 ASP cc_start: 0.6667 (p0) cc_final: 0.6466 (p0) REVERT: B 213 VAL cc_start: 0.7802 (m) cc_final: 0.7480 (t) REVERT: B 228 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.7069 (p0) REVERT: B 233 CYS cc_start: 0.6869 (t) cc_final: 0.6601 (t) REVERT: B 247 ASP cc_start: 0.6516 (t0) cc_final: 0.6266 (t0) REVERT: B 254 ASP cc_start: 0.6356 (t0) cc_final: 0.6082 (t0) REVERT: R 78 PHE cc_start: 0.7493 (t80) cc_final: 0.7270 (t80) REVERT: R 116 ILE cc_start: 0.7903 (tp) cc_final: 0.7495 (tp) REVERT: R 236 ILE cc_start: 0.7482 (tp) cc_final: 0.7159 (tp) outliers start: 29 outliers final: 21 residues processed: 217 average time/residue: 0.2381 time to fit residues: 68.6305 Evaluate side-chains 226 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9124 Z= 0.237 Angle : 0.595 7.412 12369 Z= 0.311 Chirality : 0.042 0.202 1402 Planarity : 0.005 0.063 1552 Dihedral : 5.415 58.365 1238 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.77 % Allowed : 17.73 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1112 helix: 0.98 (0.27), residues: 394 sheet: -1.26 (0.30), residues: 279 loop : -1.08 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 241 HIS 0.005 0.001 HIS S 35 PHE 0.015 0.001 PHE S 108 TYR 0.030 0.002 TYR S 223 ARG 0.009 0.000 ARG R 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 345 LYS cc_start: 0.7769 (mmtt) cc_final: 0.7512 (mmtm) REVERT: B 133 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8110 (m) REVERT: B 147 SER cc_start: 0.8050 (m) cc_final: 0.7843 (p) REVERT: B 150 ARG cc_start: 0.7973 (mpt180) cc_final: 0.7750 (mpt180) REVERT: B 173 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7817 (p) REVERT: B 213 VAL cc_start: 0.7786 (m) cc_final: 0.7428 (t) REVERT: B 228 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7027 (p0) REVERT: B 233 CYS cc_start: 0.6853 (t) cc_final: 0.6577 (t) REVERT: B 247 ASP cc_start: 0.6459 (t0) cc_final: 0.6191 (t0) REVERT: B 254 ASP cc_start: 0.6330 (t0) cc_final: 0.6072 (t0) REVERT: B 312 ASP cc_start: 0.6838 (t0) cc_final: 0.6604 (t0) REVERT: R 116 ILE cc_start: 0.7899 (tp) cc_final: 0.7428 (tp) REVERT: R 236 ILE cc_start: 0.7339 (tp) cc_final: 0.6991 (tp) REVERT: S 128 MET cc_start: 0.7045 (mtp) cc_final: 0.6750 (mtt) REVERT: S 143 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7806 (p) outliers start: 27 outliers final: 21 residues processed: 213 average time/residue: 0.2394 time to fit residues: 67.1089 Evaluate side-chains 222 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.0470 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 340 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9124 Z= 0.190 Angle : 0.591 10.646 12369 Z= 0.306 Chirality : 0.041 0.185 1402 Planarity : 0.004 0.062 1552 Dihedral : 5.317 59.092 1238 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.97 % Allowed : 17.11 % Favored : 79.92 % 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: -0.60 (0.26), residues: 1112 helix: 1.10 (0.27), residues: 394 sheet: -1.25 (0.30), residues: 281 loop : -1.08 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 241 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE R 90 TYR 0.026 0.001 TYR S 223 ARG 0.008 0.000 ARG R 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 345 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7507 (mmtm) REVERT: B 133 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8098 (m) REVERT: B 173 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7809 (p) REVERT: B 228 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6994 (p0) REVERT: B 247 ASP cc_start: 0.6315 (t0) cc_final: 0.5966 (t0) REVERT: B 254 ASP cc_start: 0.6300 (t0) cc_final: 0.6039 (t0) REVERT: B 312 ASP cc_start: 0.6855 (t0) cc_final: 0.6614 (t0) REVERT: R 78 PHE cc_start: 0.7407 (t80) cc_final: 0.7182 (t80) REVERT: R 116 ILE cc_start: 0.7912 (tp) cc_final: 0.7641 (tp) REVERT: S 143 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7845 (p) outliers start: 29 outliers final: 21 residues processed: 218 average time/residue: 0.2338 time to fit residues: 67.8676 Evaluate side-chains 225 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.657 > 50: distance: 41 - 61: 33.993 distance: 46 - 69: 30.885 distance: 53 - 77: 37.186 distance: 56 - 61: 34.480 distance: 57 - 83: 36.243 distance: 61 - 62: 11.418 distance: 62 - 63: 50.289 distance: 62 - 65: 63.684 distance: 63 - 64: 38.937 distance: 63 - 69: 61.801 distance: 64 - 91: 48.049 distance: 65 - 66: 57.107 distance: 66 - 67: 9.265 distance: 69 - 70: 16.854 distance: 70 - 71: 40.867 distance: 70 - 73: 51.492 distance: 71 - 72: 14.131 distance: 71 - 77: 57.939 distance: 72 - 99: 5.608 distance: 73 - 74: 29.791 distance: 74 - 75: 43.361 distance: 74 - 76: 31.681 distance: 78 - 79: 67.851 distance: 79 - 80: 23.310 distance: 79 - 83: 56.675 distance: 80 - 106: 48.199 distance: 81 - 82: 39.885 distance: 83 - 84: 31.929 distance: 84 - 85: 30.763 distance: 84 - 87: 52.041 distance: 85 - 91: 23.175 distance: 86 - 118: 3.507 distance: 87 - 89: 40.302 distance: 88 - 90: 26.688 distance: 91 - 92: 8.305 distance: 92 - 93: 26.427 distance: 93 - 99: 38.182 distance: 94 - 127: 3.264 distance: 95 - 96: 30.899 distance: 95 - 97: 14.151 distance: 96 - 98: 24.551 distance: 99 - 100: 36.660 distance: 100 - 103: 14.680 distance: 101 - 102: 41.570 distance: 102 - 135: 4.773 distance: 103 - 104: 13.999 distance: 103 - 105: 12.733 distance: 106 - 107: 38.897 distance: 107 - 108: 47.925 distance: 107 - 110: 57.143 distance: 108 - 109: 20.325 distance: 108 - 118: 13.265 distance: 109 - 146: 31.227 distance: 111 - 112: 16.572 distance: 111 - 113: 38.884 distance: 112 - 114: 14.342 distance: 115 - 116: 39.486 distance: 119 - 122: 38.575 distance: 120 - 121: 40.478 distance: 120 - 127: 40.240 distance: 122 - 123: 40.335 distance: 125 - 126: 57.803 distance: 127 - 128: 41.312 distance: 128 - 129: 41.008 distance: 128 - 131: 32.297 distance: 129 - 135: 42.024 distance: 131 - 132: 38.591 distance: 132 - 133: 40.357 distance: 135 - 136: 50.434 distance: 136 - 137: 43.806 distance: 136 - 139: 40.238 distance: 137 - 138: 23.981 distance: 137 - 146: 29.749 distance: 139 - 140: 40.643 distance: 140 - 141: 55.573 distance: 142 - 143: 56.754 distance: 143 - 144: 41.551 distance: 143 - 145: 39.988