Starting phenix.real_space_refine (version: dev) on Wed Dec 14 13:13:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/12_2022/7uzq_26916_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/12_2022/7uzq_26916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/12_2022/7uzq_26916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/12_2022/7uzq_26916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/12_2022/7uzq_26916_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/12_2022/7uzq_26916_trim_updated.pdb" } resolution = 2.17 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= 0.002 sd= 0.354 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" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 340": "OE1" <-> "OE2" Residue "L PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 202": "OE1" <-> "OE2" Residue "Q GLU 231": "OE1" <-> "OE2" Residue "Q ASP 234": "OD1" <-> "OD2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 125": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 20617 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 6022 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 5958 Classifications: {'peptide': 380} Modifications used: {'COO': 1} 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, 5958 Classifications: {'peptide': 380} Modifications used: {'COO': 1} 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: 5959 Chain: "L" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 5916 Classifications: {'peptide': 388} Modifications used: {'COO': 1, 'NH3': 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: 5943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 5943 Classifications: {'peptide': 390} Modifications used: {'COO': 1, 'NH3': 1} 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: "J" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2370 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "L" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "Q" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "J" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR K 34 " occ=0.55 ... (38 atoms not shown) pdb=" HH BTYR K 34 " occ=0.45 residue: pdb=" N APHE K 239 " occ=0.58 ... (38 atoms not shown) pdb=" HZ BPHE K 239 " occ=0.42 residue: pdb=" N ATYR K 242 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR K 242 " occ=0.47 Time building chain proxies: 12.40, per 1000 atoms: 0.60 Number of scatterers: 20617 At special positions: 0 Unit cell: (99.6, 92.96, 102.09, 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) S 69 16.00 O 2002 8.00 N 1642 7.00 C 6690 6.00 H 10214 1.00 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: 20.94 Conformation dependent library (CDL) restraints added in 2.4 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 0 sheets defined 69.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'K' and resid 12 through 31 Processing helix chain 'K' and resid 44 through 59 removed outlier: 3.757A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.735A 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 97 removed outlier: 3.741A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 129 removed outlier: 3.544A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA K 129 " --> pdb=" O ILE K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 161 Processing helix chain 'K' and resid 167 through 186 removed outlier: 4.364A pdb=" N TYR K 173 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA K 177 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE K 179 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY K 180 " --> pdb=" O ALA K 177 " (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 273 removed outlier: 3.644A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 280 Processing helix chain 'K' and resid 291 through 311 Processing helix chain 'K' and resid 327 through 347 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: 3.653A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 132 removed outlier: 3.681A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL L 132 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 161 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: 3.648A pdb=" N ILE L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 3.758A 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 261 removed outlier: 3.637A 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: 4.444A pdb=" N THR L 276 " --> pdb=" O ILE L 272 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU L 277 " --> pdb=" O GLN L 273 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA L 278 " --> pdb=" O ASN L 274 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLY L 279 " --> pdb=" O ALA L 275 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLY L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 320 removed outlier: 4.381A 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: 4.023A pdb=" N THR Q 70 " --> pdb=" O GLY Q 66 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE Q 71 " --> pdb=" O PHE Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 103 removed outlier: 3.829A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 131 removed outlier: 3.736A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 161 removed outlier: 3.607A 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: 3.586A 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: 4.314A pdb=" N THR Q 276 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU Q 277 " --> pdb=" O GLN Q 273 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA Q 278 " --> pdb=" O ASN Q 274 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY Q 279 " --> pdb=" O ALA Q 275 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLY Q 280 " --> pdb=" O THR Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 320 removed outlier: 4.358A 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 335 through 350 Processing helix chain 'Q' and resid 358 through 384 Processing helix chain 'Q' and resid 393 through 395 No H-bonds generated for 'chain 'Q' and resid 393 through 395' Processing helix chain 'Q' and resid 399 through 401 No H-bonds generated for 'chain 'Q' and resid 399 through 401' Processing helix chain 'J' and resid 12 through 22 Processing helix chain 'J' and resid 25 through 33 Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 58 through 66 Processing helix chain 'J' and resid 81 through 88 Processing helix chain 'J' and resid 91 through 99 Processing helix chain 'J' and resid 114 through 120 Processing helix chain 'J' and resid 124 through 133 Processing helix chain 'J' and resid 147 through 153 Processing helix chain 'J' and resid 157 through 166 627 hydrogen bonds defined for protein. 1845 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: 8.84 Time building geometry restraints manager: 21.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10198 1.03 - 1.23: 273 1.23 - 1.43: 4061 1.43 - 1.62: 5979 1.62 - 1.82: 122 Bond restraints: 20633 Sorted by residual: bond pdb=" C ALA Q 364 " pdb=" O ALA Q 364 " ideal model delta sigma weight residual 1.236 1.170 0.067 1.15e-02 7.56e+03 3.35e+01 bond pdb=" C ALA Q 287 " pdb=" O ALA Q 287 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.15e-02 7.56e+03 1.88e+01 bond pdb=" C SER Q 171 " pdb=" O SER Q 171 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.16e-02 7.43e+03 1.64e+01 bond pdb=" C MET Q 8 " pdb=" O MET Q 8 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.19e-02 7.06e+03 1.63e+01 bond pdb=" C ASP K 404 " pdb=" O ASP K 404 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.25e-02 6.40e+03 1.43e+01 ... (remaining 20628 not shown) Histogram of bond angle deviations from ideal: 96.72 - 104.23: 161 104.23 - 111.74: 23294 111.74 - 119.24: 5276 119.24 - 126.75: 8411 126.75 - 134.26: 140 Bond angle restraints: 37282 Sorted by residual: angle pdb=" N MET Q 172 " pdb=" CA MET Q 172 " pdb=" C MET Q 172 " ideal model delta sigma weight residual 111.36 118.76 -7.40 1.09e+00 8.42e-01 4.61e+01 angle pdb=" CA HIS J 123 " pdb=" C HIS J 123 " pdb=" O HIS J 123 " ideal model delta sigma weight residual 122.37 116.80 5.57 1.15e+00 7.56e-01 2.34e+01 angle pdb=" N ALA Q 353 " pdb=" CA ALA Q 353 " pdb=" C ALA Q 353 " ideal model delta sigma weight residual 111.28 106.09 5.19 1.09e+00 8.42e-01 2.27e+01 angle pdb=" N SER Q 171 " pdb=" CA SER Q 171 " pdb=" C SER Q 171 " ideal model delta sigma weight residual 111.02 105.23 5.79 1.22e+00 6.72e-01 2.25e+01 angle pdb=" CA VAL K 406 " pdb=" C VAL K 406 " pdb=" O VAL K 406 " ideal model delta sigma weight residual 120.95 116.60 4.35 1.04e+00 9.25e-01 1.75e+01 ... (remaining 37277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.22: 7683 24.22 - 48.45: 414 48.45 - 72.67: 71 72.67 - 96.90: 15 96.90 - 121.12: 1 Dihedral angle restraints: 8184 sinusoidal: 3614 harmonic: 4570 Sorted by residual: 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 63.52 -121.12 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" CA TRP L 403 " pdb=" C TRP L 403 " pdb=" N LYS L 404 " pdb=" CA LYS L 404 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.61e+01 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 -131.66 9.06 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 8181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1305 0.055 - 0.111: 306 0.111 - 0.166: 58 0.166 - 0.222: 10 0.222 - 0.277: 5 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CA VAL K 249 " pdb=" N VAL K 249 " pdb=" C VAL K 249 " pdb=" CB VAL K 249 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.92e+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 2.48 -0.28 2.00e-01 2.50e+01 1.91e+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 2.81 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1681 not shown) Planarity restraints: 2996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN Q 361 " 0.248 2.00e-02 2.50e+03 3.06e-01 1.40e+03 pdb=" CD GLN Q 361 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN Q 361 " -0.242 2.00e-02 2.50e+03 pdb=" NE2 GLN Q 361 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN Q 361 " -0.464 2.00e-02 2.50e+03 pdb="HE22 GLN Q 361 " 0.475 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 120 " -0.094 2.00e-02 2.50e+03 9.67e-02 1.40e+02 pdb=" CD GLN J 120 " 0.012 2.00e-02 2.50e+03 pdb=" OE1 GLN J 120 " 0.085 2.00e-02 2.50e+03 pdb=" NE2 GLN J 120 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN J 120 " 0.139 2.00e-02 2.50e+03 pdb="HE22 GLN J 120 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN K 405 " -0.062 2.00e-02 2.50e+03 6.53e-02 6.40e+01 pdb=" CD GLN K 405 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN K 405 " 0.060 2.00e-02 2.50e+03 pdb=" NE2 GLN K 405 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN K 405 " 0.095 2.00e-02 2.50e+03 pdb="HE22 GLN K 405 " -0.096 2.00e-02 2.50e+03 ... (remaining 2993 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 2637 2.25 - 2.84: 47031 2.84 - 3.43: 62410 3.43 - 4.01: 85041 4.01 - 4.60: 128418 Nonbonded interactions: 325537 Sorted by model distance: nonbonded pdb=" O PHE L 67 " pdb=" HG1 THR L 70 " model vdw 1.667 1.850 nonbonded pdb=" H VAL L 405 " pdb=" O HOH L 615 " model vdw 1.697 1.850 nonbonded pdb=" O PHE K 28 " pdb=" HG1 THR K 32 " model vdw 1.702 1.850 nonbonded pdb="HH22 ARG K 154 " pdb=" O HOH K 502 " model vdw 1.706 1.850 nonbonded pdb=" HE ARG L 264 " pdb=" O HOH K 503 " model vdw 1.708 1.850 ... (remaining 325532 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 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1 or name HE2 or name HZ )) or resid 49 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: 5 Type Number sf(0) Gaussians S 69 5.16 5 C 6690 2.51 5 N 1642 2.21 5 O 2002 1.98 5 H 10214 0.53 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=0.42 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: 0.710 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: 0.370 Extract box with map and model: 6.040 Check model and map are aligned: 0.340 Convert atoms to be neutral: 0.180 Process input model: 76.810 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 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 0.088 10419 Z= 0.421 Angle : 0.922 7.403 14183 Z= 0.608 Chirality : 0.051 0.277 1684 Planarity : 0.006 0.094 1726 Dihedral : 16.210 121.121 3556 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.78 % Favored : 97.99 % Rotamer Outliers : 2.27 % 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 (0.23), residues: 1301 helix: 1.94 (0.17), residues: 923 sheet: None (None), residues: 0 loop : 0.27 (0.32), residues: 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 1.549 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 196 average time/residue: 2.0311 time to fit residues: 440.4310 Evaluate side-chains 189 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 1.725 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 1.0405 time to fit residues: 7.0803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 389 ASN L 58 HIS Q 104 GLN ** J 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 10419 Z= 0.325 Angle : 0.655 6.336 14183 Z= 0.359 Chirality : 0.041 0.133 1684 Planarity : 0.005 0.055 1726 Dihedral : 6.121 108.436 1408 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.78 % Favored : 98.14 % Rotamer Outliers : 3.31 % 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: 1.88 (0.23), residues: 1301 helix: 1.72 (0.17), residues: 924 sheet: None (None), residues: 0 loop : 0.18 (0.31), residues: 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.855 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 193 average time/residue: 2.0183 time to fit residues: 430.6412 Evaluate side-chains 192 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 7 average time/residue: 0.5570 time to fit residues: 7.2210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 117 optimal weight: 40.0000 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 233 GLN L 58 HIS Q 104 GLN ** J 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 10419 Z= 0.316 Angle : 0.647 6.007 14183 Z= 0.354 Chirality : 0.041 0.130 1684 Planarity : 0.005 0.055 1726 Dihedral : 6.049 111.008 1408 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.70 % Favored : 98.22 % Rotamer Outliers : 3.31 % 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: 1.67 (0.22), residues: 1301 helix: 1.59 (0.16), residues: 924 sheet: None (None), residues: 0 loop : 0.05 (0.30), residues: 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.724 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 193 average time/residue: 2.0983 time to fit residues: 446.5756 Evaluate side-chains 188 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 6 average time/residue: 0.6216 time to fit residues: 6.8140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 50.0000 chunk 88 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN L 58 HIS Q 104 GLN J 162 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10419 Z= 0.192 Angle : 0.548 5.364 14183 Z= 0.299 Chirality : 0.037 0.125 1684 Planarity : 0.004 0.054 1726 Dihedral : 5.783 114.066 1408 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.78 % Favored : 98.14 % Rotamer Outliers : 2.84 % 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: 2.03 (0.23), residues: 1301 helix: 1.87 (0.17), residues: 925 sheet: None (None), residues: 0 loop : 0.12 (0.31), residues: 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.802 Fit side-chains outliers start: 29 outliers final: 19 residues processed: 191 average time/residue: 2.0106 time to fit residues: 425.4871 Evaluate side-chains 189 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 1.763 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 5 average time/residue: 0.9353 time to fit residues: 7.9613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 389 ASN L 58 HIS Q 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 10419 Z= 0.273 Angle : 0.611 5.466 14183 Z= 0.334 Chirality : 0.040 0.127 1684 Planarity : 0.005 0.054 1726 Dihedral : 5.885 111.796 1408 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.78 % Favored : 98.14 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.22), residues: 1301 helix: 1.71 (0.16), residues: 923 sheet: None (None), residues: 0 loop : 0.05 (0.31), residues: 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 1.704 Fit side-chains outliers start: 31 outliers final: 21 residues processed: 191 average time/residue: 2.0397 time to fit residues: 431.0295 Evaluate side-chains 190 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 6 average time/residue: 0.5634 time to fit residues: 6.7414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN L 58 HIS Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10419 Z= 0.228 Angle : 0.576 5.672 14183 Z= 0.314 Chirality : 0.038 0.126 1684 Planarity : 0.004 0.054 1726 Dihedral : 5.805 113.289 1408 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % 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: 1.96 (0.23), residues: 1301 helix: 1.82 (0.17), residues: 925 sheet: None (None), residues: 0 loop : 0.10 (0.31), residues: 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.724 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 188 average time/residue: 2.0609 time to fit residues: 427.4858 Evaluate side-chains 188 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 2 average time/residue: 0.2709 time to fit residues: 3.1238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 389 ASN L 58 HIS Q 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10419 Z= 0.244 Angle : 0.589 5.483 14183 Z= 0.322 Chirality : 0.039 0.126 1684 Planarity : 0.004 0.054 1726 Dihedral : 5.818 112.687 1408 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer Outliers : 2.65 % 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: 1.89 (0.22), residues: 1301 helix: 1.77 (0.16), residues: 923 sheet: None (None), residues: 0 loop : 0.07 (0.31), residues: 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.717 Fit side-chains outliers start: 27 outliers final: 22 residues processed: 187 average time/residue: 2.0900 time to fit residues: 430.9189 Evaluate side-chains 189 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 6 average time/residue: 1.0860 time to fit residues: 9.6339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN L 58 HIS Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10419 Z= 0.292 Angle : 0.628 5.477 14183 Z= 0.342 Chirality : 0.040 0.128 1684 Planarity : 0.005 0.054 1726 Dihedral : 5.900 111.799 1408 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.93 % Favored : 97.99 % Rotamer Outliers : 2.55 % 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: 1.77 (0.22), residues: 1301 helix: 1.68 (0.17), residues: 923 sheet: None (None), residues: 0 loop : 0.02 (0.31), residues: 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 1.816 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 20 residues processed: 189 average time/residue: 2.0022 time to fit residues: 418.3686 Evaluate side-chains 189 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 6 average time/residue: 0.3125 time to fit residues: 5.0895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 116 optimal weight: 50.0000 chunk 120 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 389 ASN L 58 HIS Q 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10419 Z= 0.271 Angle : 0.611 5.451 14183 Z= 0.333 Chirality : 0.040 0.127 1684 Planarity : 0.005 0.054 1726 Dihedral : 5.879 112.362 1408 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.93 % Favored : 97.99 % Rotamer Outliers : 2.27 % 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: 1.79 (0.22), residues: 1301 helix: 1.70 (0.17), residues: 923 sheet: None (None), residues: 0 loop : 0.01 (0.30), residues: 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 1.795 Fit side-chains outliers start: 23 outliers final: 19 residues processed: 185 average time/residue: 2.1182 time to fit residues: 433.6779 Evaluate side-chains 186 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 3 average time/residue: 0.8452 time to fit residues: 5.0739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN L 58 HIS Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 10419 Z= 0.259 Angle : 0.607 5.798 14183 Z= 0.331 Chirality : 0.039 0.127 1684 Planarity : 0.004 0.054 1726 Dihedral : 5.868 112.534 1408 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer Outliers : 2.17 % 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: 1.82 (0.23), residues: 1301 helix: 1.72 (0.17), residues: 923 sheet: None (None), residues: 0 loop : 0.02 (0.30), residues: 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.803 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 187 average time/residue: 2.0824 time to fit residues: 430.1458 Evaluate side-chains 189 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 4 average time/residue: 0.3052 time to fit residues: 4.2525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 389 ASN L 58 HIS Q 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.119664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.091143 restraints weight = 39686.910| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.12 r_work: 0.2759 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 10419 Z= 0.288 Angle : 0.627 5.551 14183 Z= 0.342 Chirality : 0.040 0.128 1684 Planarity : 0.005 0.054 1726 Dihedral : 5.909 111.969 1408 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.93 % Favored : 97.99 % Rotamer Outliers : 2.08 % 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: 1.73 (0.22), residues: 1301 helix: 1.65 (0.17), residues: 923 sheet: None (None), residues: 0 loop : -0.00 (0.30), residues: 378 =============================================================================== Job complete usr+sys time: 7719.94 seconds wall clock time: 136 minutes 15.01 seconds (8175.01 seconds total)