Starting phenix.real_space_refine on Mon Mar 18 11:01:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/03_2024/7uzq_26916_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/03_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_26916/03_2024/7uzq_26916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/03_2024/7uzq_26916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/03_2024/7uzq_26916_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzq_26916/03_2024/7uzq_26916_trim_updated.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.46, 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: 20.33 Conformation dependent library (CDL) restraints added in 2.7 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: 11.28 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: 7.91 Time building geometry restraints manager: 20.91 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: 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 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: 1.290 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: 0.280 Extract box with map and model: 5.160 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 77.970 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.380 ------------------------------------------------------------------------------- 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= 0.421 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 : 1.735 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: 2.2593 time to fit residues: 483.0118 Evaluate side-chains 190 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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: 1.9990 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: 8.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 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 ** 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: 0.8708 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10419 Z= 0.286 Angle : 0.629 6.735 14183 Z= 0.343 Chirality : 0.040 0.169 1684 Planarity : 0.005 0.055 1726 Dihedral : 7.452 54.816 1755 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.86 % Favored : 98.07 % Rotamer: Outliers : 3.12 % Allowed : 12.00 % 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: 1.98 (0.23), residues: 1301 helix: 1.80 (0.17), residues: 924 sheet: None (None), residues: 0 loop : 0.21 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 393 HIS 0.006 0.002 HIS L 154 PHE 0.023 0.003 PHE L 245 TYR 0.033 0.003 TYR Q 180 ARG 0.003 0.000 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 207 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: K 340 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6112 (mp0) REVERT: Q 1 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.4985 (pmm) outliers start: 32 outliers final: 20 residues processed: 193 average time/residue: 2.2454 time to fit residues: 472.6186 Evaluate side-chains 195 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 16 TRP Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 230 SER 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 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 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: 8.9990 chunk 117 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- 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: 0.8725 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10419 Z= 0.375 Angle : 0.682 6.280 14183 Z= 0.376 Chirality : 0.043 0.132 1684 Planarity : 0.005 0.056 1726 Dihedral : 6.927 58.468 1749 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.70 % Favored : 98.22 % Rotamer: Outliers : 3.59 % Allowed : 11.81 % Favored : 84.59 % 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: 1.57 (0.22), residues: 1301 helix: 1.52 (0.16), residues: 923 sheet: None (None), residues: 0 loop : -0.00 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP K 393 HIS 0.008 0.002 HIS J 50 PHE 0.029 0.003 PHE L 245 TYR 0.033 0.003 TYR Q 180 ARG 0.004 0.001 ARG K 71 *********************** 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 206 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 1.610 Fit side-chains REVERT: K 16 TRP cc_start: 0.7751 (OUTLIER) cc_final: 0.6879 (t-100) REVERT: K 262 GLN cc_start: 0.5369 (OUTLIER) cc_final: 0.4574 (pt0) REVERT: K 340 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: Q 1 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.5234 (pmm) REVERT: J 110 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.6967 (mppt) outliers start: 37 outliers final: 20 residues processed: 191 average time/residue: 2.3635 time to fit residues: 490.9051 Evaluate side-chains 190 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 16 TRP Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 230 SER Chi-restraints excluded: chain K residue 232 ILE 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 40.0000 chunk 88 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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: 0.8693 moved from start: 0.0775 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= 0.205 Angle : 0.554 5.513 14183 Z= 0.304 Chirality : 0.037 0.127 1684 Planarity : 0.004 0.056 1726 Dihedral : 6.239 58.165 1748 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.70 % Favored : 98.22 % Rotamer: Outliers : 2.36 % Allowed : 12.67 % 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: 1.94 (0.23), residues: 1301 helix: 1.80 (0.17), residues: 925 sheet: None (None), residues: 0 loop : 0.09 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 185 HIS 0.005 0.001 HIS L 154 PHE 0.019 0.002 PHE Q 257 TYR 0.024 0.002 TYR K 173 ARG 0.002 0.000 ARG K 71 *********************** 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 197 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: K 340 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6027 (mp0) REVERT: Q 351 MET cc_start: 0.7966 (mmp) cc_final: 0.7748 (mmt) outliers start: 24 outliers final: 11 residues processed: 186 average time/residue: 2.3701 time to fit residues: 480.4509 Evaluate side-chains 183 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG 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 330 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU 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 124 LEU 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: 9.9990 chunk 1 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 0.0970 chunk 31 optimal weight: 9.9990 overall best weight: 7.0186 ------------------------------------------------------------------------------- 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 K 389 ASN L 58 HIS Q 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.005 0.048 10419 Z= 0.314 Angle : 0.632 5.699 14183 Z= 0.348 Chirality : 0.041 0.129 1684 Planarity : 0.005 0.055 1726 Dihedral : 6.311 58.755 1737 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.78 % Favored : 98.14 % Rotamer: Outliers : 3.12 % Allowed : 11.91 % 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: 1.69 (0.22), residues: 1301 helix: 1.62 (0.16), residues: 923 sheet: None (None), residues: 0 loop : 0.01 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 185 HIS 0.006 0.002 HIS L 154 PHE 0.026 0.003 PHE L 245 TYR 0.028 0.003 TYR Q 180 ARG 0.003 0.000 ARG K 71 *********************** 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: 32 poor density : 170 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: K 262 GLN cc_start: 0.5375 (OUTLIER) cc_final: 0.4583 (pt0) REVERT: K 340 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: L 73 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8819 (pttp) REVERT: J 110 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.6976 (mppt) outliers start: 32 outliers final: 17 residues processed: 189 average time/residue: 2.3559 time to fit residues: 484.2441 Evaluate side-chains 188 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 106 VAL 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN L 58 HIS Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0835 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= 0.230 Angle : 0.569 5.310 14183 Z= 0.313 Chirality : 0.038 0.127 1684 Planarity : 0.004 0.055 1726 Dihedral : 5.875 58.226 1733 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 2.36 % Allowed : 12.67 % 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: 1.91 (0.23), residues: 1301 helix: 1.78 (0.17), residues: 925 sheet: None (None), residues: 0 loop : 0.08 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 185 HIS 0.005 0.001 HIS L 154 PHE 0.021 0.002 PHE Q 257 TYR 0.023 0.002 TYR Q 180 ARG 0.003 0.000 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 196 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.722 Fit side-chains revert: symmetry clash REVERT: K 340 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6029 (mp0) REVERT: J 110 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.6732 (mppt) outliers start: 24 outliers final: 15 residues processed: 183 average time/residue: 2.3791 time to fit residues: 473.2609 Evaluate side-chains 188 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 330 SER 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- 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: 0.8718 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10419 Z= 0.326 Angle : 0.639 5.639 14183 Z= 0.352 Chirality : 0.042 0.129 1684 Planarity : 0.005 0.056 1726 Dihedral : 6.178 55.584 1733 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.86 % Favored : 98.07 % Rotamer: Outliers : 2.65 % Allowed : 12.29 % Favored : 85.07 % 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: 1.66 (0.22), residues: 1301 helix: 1.60 (0.16), residues: 923 sheet: None (None), residues: 0 loop : -0.01 (0.30), residues: 378 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 0.027 0.003 PHE L 245 TYR 0.029 0.003 TYR Q 180 ARG 0.003 0.000 ARG K 71 *********************** 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: 27 poor density : 170 time to evaluate : 1.604 Fit side-chains REVERT: K 16 TRP cc_start: 0.7730 (OUTLIER) cc_final: 0.6838 (t-100) REVERT: K 262 GLN cc_start: 0.5342 (OUTLIER) cc_final: 0.4528 (pt0) REVERT: K 340 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: L 73 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8822 (pttp) REVERT: J 110 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.6981 (mppt) outliers start: 27 outliers final: 15 residues processed: 185 average time/residue: 2.4130 time to fit residues: 485.6549 Evaluate side-chains 188 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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 Q 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.0871 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= 0.206 Angle : 0.553 5.312 14183 Z= 0.303 Chirality : 0.038 0.128 1684 Planarity : 0.004 0.055 1726 Dihedral : 5.788 55.573 1733 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 1.89 % Allowed : 13.23 % 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: 1.98 (0.23), residues: 1301 helix: 1.83 (0.17), residues: 925 sheet: None (None), residues: 0 loop : 0.10 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 185 HIS 0.005 0.001 HIS L 154 PHE 0.020 0.002 PHE Q 257 TYR 0.021 0.002 TYR Q 180 ARG 0.002 0.000 ARG Q 195 *********************** 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 190 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.677 Fit side-chains revert: symmetry clash REVERT: K 340 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6008 (mp0) REVERT: J 110 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.6746 (mppt) outliers start: 19 outliers final: 13 residues processed: 182 average time/residue: 2.4279 time to fit residues: 480.2548 Evaluate side-chains 184 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 304 ILE 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 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 237 CYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 8.9990 chunk 116 optimal weight: 50.0000 chunk 120 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 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: 0.0853 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= 0.234 Angle : 0.574 5.296 14183 Z= 0.316 Chirality : 0.038 0.126 1684 Planarity : 0.005 0.055 1726 Dihedral : 5.821 53.943 1732 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.01 % Favored : 97.91 % Rotamer: Outliers : 2.17 % Allowed : 12.85 % 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: 1.94 (0.23), residues: 1301 helix: 1.81 (0.17), residues: 923 sheet: None (None), residues: 0 loop : 0.08 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 185 HIS 0.005 0.001 HIS L 154 PHE 0.021 0.002 PHE Q 257 TYR 0.024 0.002 TYR Q 180 ARG 0.005 0.000 ARG K 11 *********************** 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: 22 poor density : 171 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: K 16 TRP cc_start: 0.7653 (OUTLIER) cc_final: 0.6720 (t-100) REVERT: K 340 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6025 (mp0) REVERT: L 73 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8797 (pttp) REVERT: J 110 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.6738 (mppt) outliers start: 22 outliers final: 16 residues processed: 185 average time/residue: 2.4364 time to fit residues: 489.8544 Evaluate side-chains 191 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG 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 304 ILE 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 K residue 374 ILE Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 237 CYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 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 389 ASN L 58 HIS L 394 GLN Q 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10419 Z= 0.322 Angle : 0.641 5.520 14183 Z= 0.352 Chirality : 0.041 0.129 1684 Planarity : 0.005 0.055 1726 Dihedral : 6.084 52.433 1732 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.93 % Favored : 97.99 % Rotamer: Outliers : 2.17 % Allowed : 13.14 % 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: 1.67 (0.22), residues: 1301 helix: 1.61 (0.16), residues: 923 sheet: None (None), residues: 0 loop : -0.03 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 0.007 0.001 ARG K 11 ********************** 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 : 1.636 Fit side-chains REVERT: K 16 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.6826 (t-100) REVERT: K 340 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: L 73 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8820 (pttp) REVERT: Q 321 LYS cc_start: 0.8207 (mppt) cc_final: 0.7846 (mppt) REVERT: J 110 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.6711 (mppt) outliers start: 22 outliers final: 15 residues processed: 183 average time/residue: 2.4018 time to fit residues: 477.6720 Evaluate side-chains 186 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG 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 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 199 GLU Chi-restraints excluded: chain L residue 306 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 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 L 58 HIS Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.091340 restraints weight = 39925.930| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.14 r_work: 0.2766 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0883 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= 0.250 Angle : 0.590 5.331 14183 Z= 0.324 Chirality : 0.039 0.126 1684 Planarity : 0.005 0.055 1726 Dihedral : 5.891 53.552 1732 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 1.98 % Allowed : 13.42 % Favored : 84.59 % 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: 1.72 (0.17), residues: 923 sheet: None (None), residues: 0 loop : 0.01 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 185 HIS 0.005 0.001 HIS L 154 PHE 0.022 0.002 PHE Q 257 TYR 0.024 0.003 TYR Q 180 ARG 0.005 0.000 ARG K 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8393.41 seconds wall clock time: 148 minutes 4.73 seconds (8884.73 seconds total)