Starting phenix.real_space_refine (version: dev) on Mon Dec 12 05:16:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/12_2022/8csx_26974_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/12_2022/8csx_26974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/12_2022/8csx_26974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/12_2022/8csx_26974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/12_2022/8csx_26974_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csx_26974/12_2022/8csx_26974_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.322 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9116 Number of models: 1 Model: "" Number of chains: 8 Chain: "K" Number of atoms: 2943 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2962 Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2938 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2954 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'AJP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 43 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR K 34 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.45 residue: pdb=" N ATYR K 242 " occ=0.53 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.47 Time building chain proxies: 6.92, per 1000 atoms: 0.76 Number of scatterers: 9116 At special positions: 0 Unit cell: (91.3, 89.64, 92.13, 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 66 16.00 O 1685 8.00 N 1424 7.00 C 5941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 1 sheets defined 71.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'K' and resid 12 through 31 Processing helix chain 'K' and resid 44 through 59 removed outlier: 3.889A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 65 Processing helix chain 'K' and resid 73 through 98 removed outlier: 3.647A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU K 93 " --> pdb=" O GLN K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 129 removed outlier: 3.592A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA K 129 " --> pdb=" O ILE K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 160 Processing helix chain 'K' and resid 167 through 186 removed outlier: 3.592A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS K 171 " --> pdb=" O ASN K 168 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE K 172 " --> pdb=" O LEU K 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR K 173 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE K 175 " --> pdb=" O PHE K 172 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE K 179 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 224 Proline residue: K 221 - end of helix Processing helix chain 'K' and resid 231 through 255 Processing helix chain 'K' and resid 267 through 281 removed outlier: 3.628A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU K 275 " --> pdb=" O HIS K 271 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA K 276 " --> pdb=" O SER K 272 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLY K 277 " --> pdb=" O ALA K 273 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY K 278 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 311 Processing helix chain 'K' and resid 327 through 349 removed outlier: 3.602A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU K 349 " --> pdb=" O VAL K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 388 Processing helix chain 'K' and resid 391 through 393 No H-bonds generated for 'chain 'K' and resid 391 through 393' Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 404 through 406 No H-bonds generated for 'chain 'K' and resid 404 through 406' Processing helix chain 'L' and resid 4 through 23 Processing helix chain 'L' and resid 51 through 62 Processing helix chain 'L' and resid 64 through 68 Processing helix chain 'L' and resid 76 through 103 removed outlier: 3.739A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 132 removed outlier: 3.711A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL L 132 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 161 removed outlier: 3.639A pdb=" N VAL L 150 " --> pdb=" O ILE L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 192 through 194 No H-bonds generated for 'chain 'L' and resid 192 through 194' Processing helix chain 'L' and resid 205 through 227 removed outlier: 3.743A pdb=" N ILE L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 234 through 260 removed outlier: 3.714A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 265 No H-bonds generated for 'chain 'L' and resid 263 through 265' Processing helix chain 'L' and resid 269 through 282 removed outlier: 4.290A pdb=" N THR L 276 " --> pdb=" O ILE L 272 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU L 277 " --> pdb=" O GLN L 273 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA L 278 " --> pdb=" O ASN L 274 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY L 279 " --> pdb=" O ALA L 275 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLY L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 320 removed outlier: 4.546A pdb=" N THR L 315 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Proline residue: L 316 - end of helix Processing helix chain 'L' and resid 330 through 333 No H-bonds generated for 'chain 'L' and resid 330 through 333' Processing helix chain 'L' and resid 335 through 350 Processing helix chain 'L' and resid 358 through 383 Processing helix chain 'L' and resid 399 through 401 No H-bonds generated for 'chain 'L' and resid 399 through 401' Processing helix chain 'Q' and resid 4 through 23 Processing helix chain 'Q' and resid 47 through 62 Proline residue: Q 52 - end of helix Processing helix chain 'Q' and resid 64 through 71 removed outlier: 3.621A pdb=" N MET Q 69 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR Q 70 " --> pdb=" O GLY Q 66 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE Q 71 " --> pdb=" O PHE Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 103 removed outlier: 3.812A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 131 removed outlier: 3.717A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 161 removed outlier: 3.688A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 188 Processing helix chain 'Q' and resid 192 through 194 No H-bonds generated for 'chain 'Q' and resid 192 through 194' Processing helix chain 'Q' and resid 205 through 227 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 234 through 261 removed outlier: 3.716A pdb=" N LEU Q 252 " --> pdb=" O ALA Q 248 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 265 No H-bonds generated for 'chain 'Q' and resid 263 through 265' Processing helix chain 'Q' and resid 269 through 282 removed outlier: 4.438A pdb=" N THR Q 276 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU Q 277 " --> pdb=" O GLN Q 273 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA Q 278 " --> pdb=" O ASN Q 274 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY Q 279 " --> pdb=" O ALA Q 275 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY Q 280 " --> pdb=" O THR Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 320 removed outlier: 4.513A pdb=" N THR Q 315 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Proline residue: Q 316 - end of helix Processing helix chain 'Q' and resid 330 through 333 No H-bonds generated for 'chain 'Q' and resid 330 through 333' Processing helix chain 'Q' and resid 336 through 350 Processing helix chain 'Q' and resid 358 through 384 Processing helix chain 'Q' and resid 399 through 401 No H-bonds generated for 'chain 'Q' and resid 399 through 401' Processing sheet with id= A, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.119A pdb=" N VAL K 106 " --> pdb=" O HIS K 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 572 hydrogen bonds defined for protein. 1684 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: 2.74 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1413 1.32 - 1.44: 2492 1.44 - 1.57: 5177 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 9199 Sorted by residual: bond pdb=" C PRO Q 293 " pdb=" O PRO Q 293 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.26e-02 6.30e+03 1.01e+01 bond pdb=" N VAL Q 373 " pdb=" CA VAL Q 373 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.02e+00 bond pdb=" N TYR Q 180 " pdb=" CA TYR Q 180 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.97e+00 bond pdb=" N LEU Q 383 " pdb=" CA LEU Q 383 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.28e-02 6.10e+03 7.70e+00 bond pdb=" N ILE Q 188 " pdb=" CA ILE Q 188 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.13e+00 ... (remaining 9194 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.98: 176 104.98 - 112.31: 4795 112.31 - 119.64: 3069 119.64 - 126.97: 4376 126.97 - 134.30: 112 Bond angle restraints: 12528 Sorted by residual: angle pdb=" N LEU Q 189 " pdb=" CA LEU Q 189 " pdb=" C LEU Q 189 " ideal model delta sigma weight residual 113.02 107.62 5.40 1.20e+00 6.94e-01 2.03e+01 angle pdb=" N ALA Q 353 " pdb=" CA ALA Q 353 " pdb=" C ALA Q 353 " ideal model delta sigma weight residual 111.28 106.39 4.89 1.09e+00 8.42e-01 2.01e+01 angle pdb=" C ARG Q 323 " pdb=" N ILE Q 324 " pdb=" CA ILE Q 324 " ideal model delta sigma weight residual 123.12 117.34 5.78 1.30e+00 5.92e-01 1.98e+01 angle pdb=" CA TYR Q 180 " pdb=" C TYR Q 180 " pdb=" O TYR Q 180 " ideal model delta sigma weight residual 120.55 116.12 4.43 1.06e+00 8.90e-01 1.75e+01 angle pdb=" C TYR Q 180 " pdb=" CA TYR Q 180 " pdb=" CB TYR Q 180 " ideal model delta sigma weight residual 110.79 117.41 -6.62 1.66e+00 3.63e-01 1.59e+01 ... (remaining 12523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 4974 24.16 - 48.32: 214 48.32 - 72.48: 31 72.48 - 96.64: 4 96.64 - 120.80: 1 Dihedral angle restraints: 5224 sinusoidal: 1930 harmonic: 3294 Sorted by residual: dihedral pdb=" C TYR Q 180 " pdb=" N TYR Q 180 " pdb=" CA TYR Q 180 " pdb=" CB TYR Q 180 " ideal model delta harmonic sigma weight residual -122.60 -134.06 11.46 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" C02 AJP Q 501 " pdb=" C85 AJP Q 501 " pdb=" O84 AJP Q 501 " pdb=" C05 AJP Q 501 " ideal model delta sinusoidal sigma weight residual -57.60 63.20 -120.80 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA TRP Q 403 " pdb=" C TRP Q 403 " pdb=" N LYS Q 404 " pdb=" CA LYS Q 404 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1263 0.067 - 0.134: 197 0.134 - 0.202: 22 0.202 - 0.269: 7 0.269 - 0.336: 2 Chirality restraints: 1491 Sorted by residual: chirality pdb=" CA TYR Q 180 " pdb=" N TYR Q 180 " pdb=" C TYR Q 180 " pdb=" CB TYR Q 180 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C11 AJP Q 501 " pdb=" C10 AJP Q 501 " pdb=" C12 AJP Q 501 " pdb=" C16 AJP Q 501 " both_signs ideal model delta sigma weight residual False 2.20 2.49 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C08 AJP Q 502 " pdb=" C07 AJP Q 502 " pdb=" C10 AJP Q 502 " pdb=" O09 AJP Q 502 " both_signs ideal model delta sigma weight residual False 2.56 2.82 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1488 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 384 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C LYS Q 384 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS Q 384 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU Q 385 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Q 324 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C ILE Q 324 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE Q 324 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS Q 325 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 345 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C GLY Q 345 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY Q 345 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE Q 346 " -0.013 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1047 2.75 - 3.28: 9687 3.28 - 3.82: 17802 3.82 - 4.36: 21412 4.36 - 4.90: 35104 Nonbonded interactions: 85052 Sorted by model distance: nonbonded pdb=" OD2 ASP Q 399 " pdb=" O HOH Q 601 " model vdw 2.208 2.440 nonbonded pdb=" OD1 ASP Q 398 " pdb=" OG SER Q 400 " model vdw 2.226 2.440 nonbonded pdb=" O TYR K 178 " pdb=" OG1 THR K 182 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR L 408 " pdb=" O HOH L 601 " model vdw 2.242 2.440 nonbonded pdb=" O LYS L 404 " pdb=" O HOH L 602 " model vdw 2.266 2.440 ... (remaining 85047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'L' and resid 1 through 409) selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5941 2.51 5 N 1424 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.020 Extract box with map and model: 4.740 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 29.540 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 9199 Z= 0.364 Angle : 0.787 9.260 12528 Z= 0.483 Chirality : 0.053 0.336 1491 Planarity : 0.006 0.055 1505 Dihedral : 13.618 120.799 3120 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.67 % Favored : 98.24 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.10 % 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: 1.76 (0.24), residues: 1143 helix: 1.68 (0.17), residues: 815 sheet: None (None), residues: 0 loop : -0.01 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 214 time to evaluate : 0.976 Fit side-chains outliers start: 36 outliers final: 9 residues processed: 233 average time/residue: 1.1131 time to fit residues: 278.0197 Evaluate side-chains 191 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.8506 time to fit residues: 5.0865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN K 49 GLN K 260 HIS L 58 HIS Q 55 GLN Q 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9199 Z= 0.254 Angle : 0.593 7.745 12528 Z= 0.317 Chirality : 0.042 0.136 1491 Planarity : 0.005 0.057 1505 Dihedral : 5.959 105.680 1243 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 4.18 % 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: 1.87 (0.24), residues: 1143 helix: 1.77 (0.17), residues: 811 sheet: None (None), residues: 0 loop : 0.00 (0.33), residues: 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 1.029 Fit side-chains outliers start: 39 outliers final: 19 residues processed: 199 average time/residue: 1.1556 time to fit residues: 246.1870 Evaluate side-chains 204 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 9 residues processed: 11 average time/residue: 0.5114 time to fit residues: 7.8072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.194 Angle : 0.540 7.036 12528 Z= 0.288 Chirality : 0.039 0.130 1491 Planarity : 0.005 0.043 1505 Dihedral : 5.804 105.881 1243 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 3.43 % 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: 2.09 (0.24), residues: 1143 helix: 1.93 (0.17), residues: 815 sheet: None (None), residues: 0 loop : 0.09 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 1.074 Fit side-chains outliers start: 32 outliers final: 15 residues processed: 204 average time/residue: 1.1399 time to fit residues: 249.5929 Evaluate side-chains 200 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 0.5702 time to fit residues: 5.9885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.193 Angle : 0.534 6.903 12528 Z= 0.284 Chirality : 0.039 0.127 1491 Planarity : 0.004 0.042 1505 Dihedral : 5.765 105.556 1243 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 3.33 % 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: 2.16 (0.24), residues: 1143 helix: 1.99 (0.17), residues: 815 sheet: None (None), residues: 0 loop : 0.10 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 1.100 Fit side-chains outliers start: 31 outliers final: 18 residues processed: 200 average time/residue: 1.1753 time to fit residues: 251.9539 Evaluate side-chains 207 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 8 residues processed: 10 average time/residue: 0.5631 time to fit residues: 7.5868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.0170 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9199 Z= 0.219 Angle : 0.557 7.217 12528 Z= 0.296 Chirality : 0.040 0.136 1491 Planarity : 0.005 0.043 1505 Dihedral : 5.814 104.926 1243 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 2.90 % 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: 2.08 (0.24), residues: 1143 helix: 1.92 (0.17), residues: 815 sheet: None (None), residues: 0 loop : 0.10 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 1.072 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 202 average time/residue: 1.1674 time to fit residues: 252.3691 Evaluate side-chains 202 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 0.3263 time to fit residues: 3.6303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9199 Z= 0.290 Angle : 0.616 7.716 12528 Z= 0.325 Chirality : 0.043 0.145 1491 Planarity : 0.005 0.043 1505 Dihedral : 5.974 104.724 1243 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 3.11 % 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: 1.87 (0.24), residues: 1143 helix: 1.77 (0.17), residues: 812 sheet: None (None), residues: 0 loop : 0.00 (0.32), residues: 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 1.035 Fit side-chains outliers start: 29 outliers final: 17 residues processed: 200 average time/residue: 1.1839 time to fit residues: 253.3143 Evaluate side-chains 204 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 9 average time/residue: 0.5913 time to fit residues: 7.3848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 9199 Z= 0.148 Angle : 0.495 6.161 12528 Z= 0.263 Chirality : 0.037 0.128 1491 Planarity : 0.004 0.044 1505 Dihedral : 5.616 104.205 1243 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 2.36 % 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: 2.31 (0.24), residues: 1143 helix: 2.13 (0.18), residues: 814 sheet: None (None), residues: 0 loop : 0.09 (0.33), residues: 329 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 1.061 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 205 average time/residue: 1.1643 time to fit residues: 256.7943 Evaluate side-chains 200 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 4 average time/residue: 0.1180 time to fit residues: 2.1583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN L 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9199 Z= 0.166 Angle : 0.516 8.556 12528 Z= 0.271 Chirality : 0.038 0.124 1491 Planarity : 0.004 0.042 1505 Dihedral : 5.613 104.057 1243 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 2.36 % 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: 2.31 (0.24), residues: 1143 helix: 2.13 (0.18), residues: 814 sheet: None (None), residues: 0 loop : 0.08 (0.33), residues: 329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 1.043 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 198 average time/residue: 1.1830 time to fit residues: 250.8579 Evaluate side-chains 200 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.1394 time to fit residues: 2.5002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 97 optimal weight: 0.0370 chunk 102 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 9199 Z= 0.252 Angle : 0.590 9.079 12528 Z= 0.310 Chirality : 0.042 0.130 1491 Planarity : 0.005 0.043 1505 Dihedral : 5.816 103.543 1243 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 2.90 % 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: 2.04 (0.24), residues: 1143 helix: 1.90 (0.17), residues: 815 sheet: None (None), residues: 0 loop : 0.06 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 1.020 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 197 average time/residue: 1.1854 time to fit residues: 249.9960 Evaluate side-chains 202 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 7 residues processed: 10 average time/residue: 0.8456 time to fit residues: 10.5689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 9199 Z= 0.274 Angle : 0.617 9.344 12528 Z= 0.325 Chirality : 0.043 0.169 1491 Planarity : 0.005 0.043 1505 Dihedral : 5.894 103.695 1243 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.61 % 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: 1.90 (0.24), residues: 1143 helix: 1.80 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -0.01 (0.33), residues: 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 0.976 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 195 average time/residue: 1.1936 time to fit residues: 249.2165 Evaluate side-chains 193 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1758 time to fit residues: 2.2380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 0.1980 chunk 5 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Q 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.118151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.099058 restraints weight = 19408.826| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.40 r_work: 0.2865 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9199 Z= 0.175 Angle : 0.535 9.246 12528 Z= 0.282 Chirality : 0.038 0.168 1491 Planarity : 0.004 0.043 1505 Dihedral : 5.686 103.683 1243 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 1.50 % 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: 2.21 (0.24), residues: 1143 helix: 2.04 (0.18), residues: 814 sheet: None (None), residues: 0 loop : 0.06 (0.33), residues: 329 =============================================================================== Job complete usr+sys time: 4205.68 seconds wall clock time: 75 minutes 12.09 seconds (4512.09 seconds total)