Starting phenix.real_space_refine on Tue Jul 23 01:03:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/07_2024/7uzq_26916_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/07_2024/7uzq_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_26916/07_2024/7uzq_26916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/07_2024/7uzq_26916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/07_2024/7uzq_26916_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/07_2024/7uzq_26916_trim.cif" } resolution = 2.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 224 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: 12.27, 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: 19.17 Conformation dependent library (CDL) restraints added in 3.6 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... Secondary structure from input PDB file: 68 helices and 3 sheets defined 78.3% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'K' and resid 11 through 31 Processing helix chain 'K' and resid 43 through 60 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 60 through 66 removed outlier: 3.769A pdb=" N THR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 99 removed outlier: 3.741A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 128 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) Processing helix chain 'K' and resid 135 through 162 Processing helix chain 'K' and resid 166 through 170 Processing helix chain 'K' and resid 171 through 187 Processing helix chain 'K' and resid 202 through 220 Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 230 through 257 removed outlier: 4.442A pdb=" N SER K 257 " --> pdb=" O ILE K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 274 removed outlier: 3.644A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 281 Processing helix chain 'K' and resid 290 through 312 removed outlier: 3.629A pdb=" N ALA K 294 " --> pdb=" O SER K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 348 removed outlier: 3.626A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 389 Processing helix chain 'K' and resid 390 through 394 removed outlier: 3.509A pdb=" N TRP K 393 " --> pdb=" O LEU K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 401 removed outlier: 3.606A pdb=" N TYR K 401 " --> pdb=" O VAL K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 407 Processing helix chain 'L' and resid 3 through 23 Processing helix chain 'L' and resid 50 through 63 Processing helix chain 'L' and resid 63 through 69 Processing helix chain 'L' and resid 70 through 72 No H-bonds generated for 'chain 'L' and resid 70 through 72' Processing helix chain 'L' and resid 75 through 104 removed outlier: 3.653A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 133 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 137 through 162 Processing helix chain 'L' and resid 174 through 189 Processing helix chain 'L' and resid 191 through 195 Processing helix chain 'L' and resid 204 through 228 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 233 through 262 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 266 Processing helix chain 'L' and resid 268 through 275 Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.626A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 321 removed outlier: 3.502A pdb=" N GLY L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) 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 329 through 334 Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 357 through 384 Processing helix chain 'L' and resid 398 through 402 Processing helix chain 'Q' and resid 3 through 23 Processing helix chain 'Q' and resid 47 through 63 Proline residue: Q 52 - end of helix Processing helix chain 'Q' and resid 63 through 69 Processing helix chain 'Q' and resid 70 through 72 No H-bonds generated for 'chain 'Q' and resid 70 through 72' Processing helix chain 'Q' and resid 75 through 104 removed outlier: 3.829A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 133 removed outlier: 3.736A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL Q 132 " --> pdb=" O SER Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 162 removed outlier: 3.607A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 189 Processing helix chain 'Q' and resid 191 through 195 Processing helix chain 'Q' and resid 204 through 228 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 233 through 262 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 266 Processing helix chain 'Q' and resid 268 through 275 Processing helix chain 'Q' and resid 277 through 283 Processing helix chain 'Q' and resid 291 through 321 removed outlier: 3.627A pdb=" N GLY Q 295 " --> pdb=" O ILE Q 291 " (cutoff:3.500A) 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 329 through 334 Processing helix chain 'Q' and resid 334 through 351 Processing helix chain 'Q' and resid 357 through 385 removed outlier: 3.804A pdb=" N LEU Q 385 " --> pdb=" O LEU Q 381 " (cutoff:3.500A) Processing helix chain 'Q' and resid 392 through 396 Processing helix chain 'Q' and resid 398 through 402 Processing helix chain 'J' and resid 12 through 23 Processing helix chain 'J' and resid 24 through 34 Processing helix chain 'J' and resid 47 through 56 Processing helix chain 'J' and resid 57 through 67 Processing helix chain 'J' and resid 80 through 89 Processing helix chain 'J' and resid 90 through 100 Processing helix chain 'J' and resid 113 through 121 Processing helix chain 'J' and resid 123 through 133 Processing helix chain 'J' and resid 146 through 154 Processing helix chain 'J' and resid 156 through 167 Processing sheet with id=AA1, first strand: chain 'K' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AA3, first strand: chain 'Q' and resid 24 through 25 734 hydrogen bonds defined for protein. 2151 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: 8.59 Time building geometry restraints manager: 20.09 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: 9214 24.22 - 48.45: 522 48.45 - 72.67: 211 72.67 - 96.90: 23 96.90 - 121.12: 9 Dihedral angle restraints: 9979 sinusoidal: 5409 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=" O34 AJP Q 502 " pdb=" C28 AJP Q 502 " pdb=" C29 AJP Q 502 " pdb=" O77 AJP Q 502 " ideal model delta sinusoidal sigma weight residual -58.96 61.69 -120.65 1 3.00e+01 1.11e-03 1.61e+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 ... (remaining 9976 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: 2585 2.25 - 2.84: 46961 2.84 - 3.43: 62306 3.43 - 4.01: 84873 4.01 - 4.60: 128279 Nonbonded interactions: 325004 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 324999 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 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.340 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 75.250 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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= 0.410 Angle : 0.922 7.403 14183 Z= 0.608 Chirality : 0.051 0.277 1684 Planarity : 0.006 0.094 1726 Dihedral : 17.122 121.121 3876 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.78 % Favored : 97.99 % Rotamer: Outliers : 2.27 % Allowed : 12.95 % Favored : 84.78 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 220 HIS 0.011 0.002 HIS J 162 PHE 0.020 0.003 PHE L 245 TYR 0.042 0.003 TYR Q 180 ARG 0.011 0.001 ARG Q 195 *********************** 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 : 1.504 Fit side-chains REVERT: K 329 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.6166 (t-90) outliers start: 23 outliers final: 15 residues processed: 196 average time/residue: 2.2496 time to fit residues: 481.3616 Evaluate side-chains 190 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 311 CYS Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 333 SER Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 237 CYS Chi-restraints excluded: chain Q residue 294 PHE Chi-restraints excluded: chain Q residue 349 VAL Chi-restraints excluded: chain J residue 71 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 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: 6.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0650 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= 0.301 Angle : 0.651 7.077 14183 Z= 0.358 Chirality : 0.041 0.158 1684 Planarity : 0.005 0.056 1726 Dihedral : 7.682 54.885 1755 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.62 % Favored : 98.30 % Rotamer: Outliers : 3.12 % Allowed : 12.19 % Favored : 84.69 % 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: 2.00 (0.23), residues: 1301 helix: 1.87 (0.17), residues: 924 sheet: None (None), residues: 0 loop : 0.05 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 185 HIS 0.007 0.002 HIS L 154 PHE 0.024 0.003 PHE L 245 TYR 0.034 0.003 TYR Q 180 ARG 0.004 0.001 ARG K 71 *********************** 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: 32 poor density : 176 time to evaluate : 1.696 Fit side-chains revert: symmetry clash REVERT: K 340 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: Q 1 MET cc_start: 0.5744 (OUTLIER) cc_final: 0.4942 (pmm) outliers start: 32 outliers final: 18 residues processed: 193 average time/residue: 2.2444 time to fit residues: 473.9456 Evaluate side-chains 194 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 311 CYS Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 333 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 117 optimal weight: 50.0000 chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 ** J 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10419 Z= 0.335 Angle : 0.666 5.512 14183 Z= 0.370 Chirality : 0.042 0.131 1684 Planarity : 0.005 0.056 1726 Dihedral : 6.706 57.806 1745 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.01 % Favored : 97.91 % Rotamer: Outliers : 3.59 % Allowed : 11.72 % Favored : 84.69 % 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: 1.75 (0.22), residues: 1301 helix: 1.70 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -0.09 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 185 HIS 0.007 0.002 HIS J 50 PHE 0.027 0.003 PHE L 245 TYR 0.032 0.003 TYR Q 180 ARG 0.004 0.001 ARG K 11 *********************** 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 210 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: K 262 GLN cc_start: 0.5412 (OUTLIER) cc_final: 0.4610 (pt0) REVERT: K 340 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6098 (mp0) REVERT: Q 1 MET cc_start: 0.5799 (OUTLIER) cc_final: 0.5160 (pmm) REVERT: J 110 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6962 (mppt) REVERT: J 145 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8440 (m-80) outliers start: 37 outliers final: 19 residues processed: 194 average time/residue: 2.3266 time to fit residues: 492.0945 Evaluate side-chains 196 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 333 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 145 PHE 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: 5.9990 chunk 61 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 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 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: 0.8699 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 0.033 10419 Z= 0.241 Angle : 0.593 5.017 14183 Z= 0.329 Chirality : 0.039 0.127 1684 Planarity : 0.005 0.055 1726 Dihedral : 6.295 58.612 1744 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.86 % Favored : 98.07 % Rotamer: Outliers : 2.65 % Allowed : 12.38 % Favored : 84.97 % 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: 1.95 (0.23), residues: 1301 helix: 1.88 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -0.09 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 185 HIS 0.005 0.001 HIS L 154 PHE 0.021 0.002 PHE Q 257 TYR 0.025 0.002 TYR Q 180 ARG 0.003 0.000 ARG K 11 *********************** 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 200 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: K 158 SER cc_start: 0.8265 (p) cc_final: 0.7971 (m) REVERT: K 340 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6046 (mp0) REVERT: Q 351 MET cc_start: 0.8017 (mmp) cc_final: 0.7813 (mmt) REVERT: J 110 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.6996 (mppt) REVERT: J 145 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8439 (m-80) outliers start: 27 outliers final: 15 residues processed: 188 average time/residue: 2.3560 time to fit residues: 482.2317 Evaluate side-chains 190 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 145 PHE 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: 6.9990 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10419 Z= 0.263 Angle : 0.609 5.259 14183 Z= 0.338 Chirality : 0.040 0.127 1684 Planarity : 0.005 0.055 1726 Dihedral : 6.160 59.212 1735 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 2.84 % Allowed : 12.38 % Favored : 84.78 % 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: 1.91 (0.23), residues: 1301 helix: 1.84 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -0.09 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 185 HIS 0.006 0.002 HIS L 154 PHE 0.023 0.002 PHE Q 257 TYR 0.026 0.003 TYR Q 180 ARG 0.004 0.000 ARG K 11 *********************** 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 201 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.618 Fit side-chains REVERT: K 16 TRP cc_start: 0.7649 (OUTLIER) cc_final: 0.6687 (t-100) REVERT: K 158 SER cc_start: 0.8271 (p) cc_final: 0.7964 (m) REVERT: K 262 GLN cc_start: 0.5375 (OUTLIER) cc_final: 0.4570 (pt0) REVERT: K 334 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7402 (tt) REVERT: K 340 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6049 (mp0) REVERT: J 110 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.6985 (mppt) REVERT: J 145 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8439 (m-80) outliers start: 29 outliers final: 16 residues processed: 190 average time/residue: 2.3375 time to fit residues: 488.1367 Evaluate side-chains 193 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 237 CYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 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 49 GLN K 159 ASN L 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10419 Z= 0.289 Angle : 0.628 5.323 14183 Z= 0.349 Chirality : 0.041 0.128 1684 Planarity : 0.005 0.055 1726 Dihedral : 6.228 57.065 1735 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 2.84 % Allowed : 12.38 % Favored : 84.78 % 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 (0.22), residues: 1301 helix: 1.77 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -0.12 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 185 HIS 0.006 0.002 HIS L 154 PHE 0.025 0.003 PHE L 245 TYR 0.027 0.003 TYR Q 180 ARG 0.005 0.001 ARG K 11 *********************** 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 199 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: K 262 GLN cc_start: 0.5350 (OUTLIER) cc_final: 0.4544 (pt0) REVERT: K 334 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7377 (tt) REVERT: K 340 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6078 (mp0) REVERT: L 73 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8809 (pttp) REVERT: J 110 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.6981 (mppt) REVERT: J 145 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8440 (m-80) outliers start: 29 outliers final: 17 residues processed: 189 average time/residue: 2.3624 time to fit residues: 485.8508 Evaluate side-chains 193 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 237 CYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10419 Z= 0.295 Angle : 0.632 5.363 14183 Z= 0.351 Chirality : 0.041 0.128 1684 Planarity : 0.005 0.054 1726 Dihedral : 6.245 55.224 1735 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 2.74 % Allowed : 12.38 % Favored : 84.88 % 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: 1.75 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -0.14 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 185 HIS 0.006 0.002 HIS L 154 PHE 0.025 0.003 PHE L 245 TYR 0.027 0.003 TYR Q 180 ARG 0.005 0.001 ARG K 11 *********************** 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 197 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 1.569 Fit side-chains REVERT: K 16 TRP cc_start: 0.7669 (OUTLIER) cc_final: 0.6717 (t-100) REVERT: K 262 GLN cc_start: 0.5324 (OUTLIER) cc_final: 0.4509 (pt0) REVERT: K 334 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7379 (tt) REVERT: K 340 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6077 (mp0) REVERT: L 73 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8813 (pttp) REVERT: J 110 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6709 (mppt) REVERT: J 145 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8442 (m-80) outliers start: 28 outliers final: 16 residues processed: 187 average time/residue: 2.3434 time to fit residues: 477.1477 Evaluate side-chains 191 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 237 CYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10419 Z= 0.331 Angle : 0.661 5.662 14183 Z= 0.367 Chirality : 0.042 0.130 1684 Planarity : 0.005 0.054 1726 Dihedral : 6.356 53.256 1735 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.24 % Favored : 97.68 % Rotamer: Outliers : 2.93 % Allowed : 12.38 % Favored : 84.69 % 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: 1.69 (0.22), residues: 1301 helix: 1.68 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -0.17 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 185 HIS 0.006 0.002 HIS L 154 PHE 0.027 0.003 PHE L 245 TYR 0.029 0.003 TYR Q 180 ARG 0.006 0.001 ARG K 11 *********************** 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 202 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.853 Fit side-chains REVERT: K 16 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.6757 (t-100) REVERT: K 262 GLN cc_start: 0.5308 (OUTLIER) cc_final: 0.4489 (pt0) REVERT: K 334 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7374 (tt) REVERT: L 73 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8817 (pttp) REVERT: Q 1 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.5118 (pmm) REVERT: J 110 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.6973 (mppt) REVERT: J 145 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8441 (m-80) outliers start: 30 outliers final: 15 residues processed: 190 average time/residue: 2.4311 time to fit residues: 502.2328 Evaluate side-chains 194 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 237 CYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 9.9990 chunk 116 optimal weight: 50.0000 chunk 120 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.8703 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10419 Z= 0.263 Angle : 0.611 5.405 14183 Z= 0.339 Chirality : 0.040 0.127 1684 Planarity : 0.005 0.055 1726 Dihedral : 6.164 53.122 1735 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 2.27 % Allowed : 13.04 % Favored : 84.69 % 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 (0.23), residues: 1301 helix: 1.82 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -0.12 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 185 HIS 0.005 0.002 HIS L 154 PHE 0.022 0.002 PHE L 245 TYR 0.026 0.003 TYR Q 180 ARG 0.003 0.000 ARG K 71 *********************** 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 193 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 158 SER cc_start: 0.8270 (p) cc_final: 0.7950 (m) REVERT: K 334 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7380 (tt) REVERT: K 340 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: L 73 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8806 (pttp) REVERT: J 145 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8439 (m-80) outliers start: 23 outliers final: 18 residues processed: 184 average time/residue: 2.4434 time to fit residues: 489.6011 Evaluate side-chains 192 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 237 CYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 145 PHE 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: 9.9990 chunk 129 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 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 L 58 HIS L 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10419 Z= 0.317 Angle : 0.655 5.556 14183 Z= 0.363 Chirality : 0.042 0.129 1684 Planarity : 0.005 0.055 1726 Dihedral : 6.328 51.334 1735 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % Rotamer: Outliers : 2.36 % Allowed : 13.33 % Favored : 84.31 % 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: 1.71 (0.22), residues: 1301 helix: 1.69 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -0.15 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 185 HIS 0.006 0.002 HIS L 154 PHE 0.026 0.003 PHE L 245 TYR 0.029 0.003 TYR Q 180 ARG 0.003 0.000 ARG K 71 ********************** 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 194 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: K 16 TRP cc_start: 0.7686 (OUTLIER) cc_final: 0.6738 (t-100) REVERT: K 334 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7383 (tt) REVERT: K 340 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6046 (mp0) REVERT: L 73 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8814 (pttp) REVERT: J 145 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8442 (m-80) outliers start: 24 outliers final: 17 residues processed: 185 average time/residue: 2.4259 time to fit residues: 488.2806 Evaluate side-chains 191 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 169 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 237 CYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 145 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.092531 restraints weight = 40141.543| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.13 r_work: 0.2779 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10419 Z= 0.214 Angle : 0.578 5.414 14183 Z= 0.319 Chirality : 0.038 0.128 1684 Planarity : 0.004 0.055 1726 Dihedral : 6.006 57.387 1735 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 2.17 % Allowed : 13.42 % Favored : 84.40 % 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: 1.94 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -0.08 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 185 HIS 0.005 0.001 HIS L 154 PHE 0.020 0.002 PHE Q 257 TYR 0.022 0.002 TYR Q 180 ARG 0.002 0.000 ARG K 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8431.52 seconds wall clock time: 146 minutes 40.56 seconds (8800.56 seconds total)