Starting phenix.real_space_refine on Mon Aug 5 20:47:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb4_19025/08_2024/8rb4_19025.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb4_19025/08_2024/8rb4_19025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb4_19025/08_2024/8rb4_19025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb4_19025/08_2024/8rb4_19025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb4_19025/08_2024/8rb4_19025.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb4_19025/08_2024/8rb4_19025.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.007 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 35 5.16 5 C 4600 2.51 5 N 1270 2.21 5 O 1345 1.98 5 H 7370 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 336": "OE1" <-> "OE2" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14620 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "D" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "F" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "I" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "J" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Time building chain proxies: 6.78, per 1000 atoms: 0.46 Number of scatterers: 14620 At special positions: 0 Unit cell: (116.48, 100.672, 84.864, 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 35 16.00 O 1345 8.00 N 1270 7.00 C 4600 6.00 H 7370 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: 11.69 Conformation dependent library (CDL) restraints added in 1.5 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 1 sheets defined 73.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 180 through 194 Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.613A pdb=" N ASN A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 242 Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 264 through 282 removed outlier: 3.564A pdb=" N LEU A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.734A pdb=" N CYS A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 removed outlier: 3.520A pdb=" N GLU A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 194 removed outlier: 3.530A pdb=" N TRP D 184 " --> pdb=" O PRO D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 208 removed outlier: 3.505A pdb=" N ARG D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 212 through 225 removed outlier: 3.606A pdb=" N ASN D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 242 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 264 through 282 removed outlier: 3.748A pdb=" N LEU D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 302 Processing helix chain 'D' and resid 306 through 319 removed outlier: 4.529A pdb=" N CYS D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'F' and resid 180 through 194 Processing helix chain 'F' and resid 198 through 208 removed outlier: 3.556A pdb=" N ARG F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 212 through 225 Processing helix chain 'F' and resid 229 through 242 Processing helix chain 'F' and resid 246 through 257 Processing helix chain 'F' and resid 264 through 282 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 302 Processing helix chain 'F' and resid 306 through 319 removed outlier: 4.203A pdb=" N GLY F 319 " --> pdb=" O LEU F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 336 Processing helix chain 'I' and resid 180 through 194 removed outlier: 3.521A pdb=" N TRP I 184 " --> pdb=" O PRO I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 208 removed outlier: 4.607A pdb=" N ARG I 204 " --> pdb=" O ALA I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 211 No H-bonds generated for 'chain 'I' and resid 209 through 211' Processing helix chain 'I' and resid 212 through 225 Processing helix chain 'I' and resid 229 through 242 Processing helix chain 'I' and resid 246 through 256 Processing helix chain 'I' and resid 264 through 282 removed outlier: 3.666A pdb=" N LEU I 275 " --> pdb=" O ARG I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 289 through 302 Processing helix chain 'I' and resid 305 through 319 removed outlier: 3.658A pdb=" N ARG I 311 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 336 removed outlier: 3.529A pdb=" N GLU I 334 " --> pdb=" O VAL I 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 194 removed outlier: 3.508A pdb=" N TRP J 184 " --> pdb=" O PRO J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 208 Processing helix chain 'J' and resid 209 through 211 No H-bonds generated for 'chain 'J' and resid 209 through 211' Processing helix chain 'J' and resid 212 through 225 Processing helix chain 'J' and resid 229 through 242 Processing helix chain 'J' and resid 246 through 257 Processing helix chain 'J' and resid 264 through 282 removed outlier: 3.577A pdb=" N LEU J 275 " --> pdb=" O ARG J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 288 No H-bonds generated for 'chain 'J' and resid 286 through 288' Processing helix chain 'J' and resid 289 through 302 Processing helix chain 'J' and resid 306 through 317 removed outlier: 3.553A pdb=" N CYS J 310 " --> pdb=" O ASN J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 323 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.571A pdb=" N VAL A 160 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR I 162 " --> pdb=" O CYS J 163 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS A 161 " --> pdb=" O VAL J 160 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR J 162 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N CYS A 163 " --> pdb=" O TYR J 162 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LYS J 164 " --> pdb=" O CYS A 163 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1299 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: 5.28 Time building geometry restraints manager: 12.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 7355 1.12 - 1.30: 1358 1.30 - 1.47: 2617 1.47 - 1.65: 3370 1.65 - 1.82: 55 Bond restraints: 14755 Sorted by residual: bond pdb=" CA ALA F 173 " pdb=" CB ALA F 173 " ideal model delta sigma weight residual 1.522 1.413 0.109 1.32e-02 5.74e+03 6.83e+01 bond pdb=" N ALA F 300 " pdb=" H ALA F 300 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CZ3 TRP A 195 " pdb=" HZ3 TRP A 195 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLY J 170 " pdb=" H GLY J 170 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NE1 TRP A 205 " pdb=" HE1 TRP A 205 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 14750 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.42: 200 104.42 - 112.14: 16621 112.14 - 119.85: 5701 119.85 - 127.57: 4175 127.57 - 135.28: 108 Bond angle restraints: 26805 Sorted by residual: angle pdb=" CD ARG D 247 " pdb=" NE ARG D 247 " pdb=" CZ ARG D 247 " ideal model delta sigma weight residual 124.40 133.79 -9.39 1.40e+00 5.10e-01 4.49e+01 angle pdb=" CD ARG I 277 " pdb=" NE ARG I 277 " pdb=" CZ ARG I 277 " ideal model delta sigma weight residual 124.40 133.54 -9.14 1.40e+00 5.10e-01 4.26e+01 angle pdb=" CA ASP A 291 " pdb=" CB ASP A 291 " pdb=" CG ASP A 291 " ideal model delta sigma weight residual 112.60 118.83 -6.23 1.00e+00 1.00e+00 3.88e+01 angle pdb=" N TYR I 258 " pdb=" CA TYR I 258 " pdb=" C TYR I 258 " ideal model delta sigma weight residual 110.41 117.63 -7.22 1.18e+00 7.18e-01 3.75e+01 angle pdb=" CA ALA F 173 " pdb=" C ALA F 173 " pdb=" N ALA F 174 " ideal model delta sigma weight residual 114.76 121.34 -6.58 1.14e+00 7.69e-01 3.33e+01 ... (remaining 26800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 6194 17.79 - 35.59: 395 35.59 - 53.38: 135 53.38 - 71.18: 106 71.18 - 88.97: 10 Dihedral angle restraints: 6840 sinusoidal: 3865 harmonic: 2975 Sorted by residual: dihedral pdb=" CA THR I 257 " pdb=" C THR I 257 " pdb=" N TYR I 258 " pdb=" CA TYR I 258 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLU J 334 " pdb=" C GLU J 334 " pdb=" N GLU J 335 " pdb=" CA GLU J 335 " ideal model delta harmonic sigma weight residual -180.00 -151.38 -28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PRO A 322 " pdb=" C PRO A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 6837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 908 0.123 - 0.245: 173 0.245 - 0.368: 18 0.368 - 0.491: 5 0.491 - 0.613: 1 Chirality restraints: 1105 Sorted by residual: chirality pdb=" CG LEU I 321 " pdb=" CB LEU I 321 " pdb=" CD1 LEU I 321 " pdb=" CD2 LEU I 321 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.61 2.00e-01 2.50e+01 9.40e+00 chirality pdb=" CB THR F 172 " pdb=" CA THR F 172 " pdb=" OG1 THR F 172 " pdb=" CG2 THR F 172 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA ALA F 174 " pdb=" N ALA F 174 " pdb=" C ALA F 174 " pdb=" CB ALA F 174 " both_signs ideal model delta sigma weight residual False 2.48 2.05 0.44 2.00e-01 2.50e+01 4.77e+00 ... (remaining 1102 not shown) Planarity restraints: 2140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 239 " 0.240 2.00e-02 2.50e+03 4.57e-01 3.14e+03 pdb=" CD GLN D 239 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN D 239 " -0.238 2.00e-02 2.50e+03 pdb=" NE2 GLN D 239 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D 239 " 0.763 2.00e-02 2.50e+03 pdb="HE22 GLN D 239 " -0.747 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 318 " 0.310 2.00e-02 2.50e+03 4.04e-01 2.45e+03 pdb=" CD GLN F 318 " -0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN F 318 " -0.304 2.00e-02 2.50e+03 pdb=" NE2 GLN F 318 " -0.005 2.00e-02 2.50e+03 pdb="HE21 GLN F 318 " 0.638 2.00e-02 2.50e+03 pdb="HE22 GLN F 318 " -0.620 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 318 " 0.272 2.00e-02 2.50e+03 2.91e-01 1.27e+03 pdb=" CD GLN A 318 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN A 318 " -0.270 2.00e-02 2.50e+03 pdb=" NE2 GLN A 318 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 318 " -0.425 2.00e-02 2.50e+03 pdb="HE22 GLN A 318 " 0.426 2.00e-02 2.50e+03 ... (remaining 2137 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 611 2.13 - 2.75: 23797 2.75 - 3.37: 42448 3.37 - 3.98: 52892 3.98 - 4.60: 78611 Nonbonded interactions: 198359 Sorted by model distance: nonbonded pdb=" O LEU A 325 " pdb="HE22 GLN D 239 " model vdw 1.517 2.450 nonbonded pdb=" HG SER F 266 " pdb=" OE1 GLU F 335 " model vdw 1.588 2.450 nonbonded pdb=" HG SER A 266 " pdb=" OE1 GLU A 335 " model vdw 1.614 2.450 nonbonded pdb=" OE1 GLU I 245 " pdb=" HG1 THR I 249 " model vdw 1.621 2.450 nonbonded pdb=" OE1 GLU D 245 " pdb=" HG1 THR D 249 " model vdw 1.625 2.450 ... (remaining 198354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' } 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=1.00 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: 0.480 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: 0.230 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 47.580 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 52.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 : 0.014 0.113 7385 Z= 0.887 Angle : 1.825 13.095 9980 Z= 1.227 Chirality : 0.099 0.613 1105 Planarity : 0.016 0.149 1295 Dihedral : 14.384 88.969 2875 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.51 % Allowed : 2.31 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 890 helix: -0.79 (0.17), residues: 607 sheet: None (None), residues: 0 loop : -0.38 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.161 0.027 TRP A 205 HIS 0.008 0.004 HIS A 219 PHE 0.052 0.014 PHE F 237 TYR 0.066 0.015 TYR I 258 ARG 0.010 0.001 ARG I 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 364 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLN cc_start: 0.8219 (mt0) cc_final: 0.7957 (mt0) REVERT: A 299 MET cc_start: 0.8927 (mtp) cc_final: 0.8639 (mtp) REVERT: D 218 MET cc_start: 0.8781 (tpp) cc_final: 0.8042 (tpt) REVERT: D 253 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7977 (mptt) REVERT: D 268 TYR cc_start: 0.8186 (t80) cc_final: 0.7978 (t80) REVERT: F 232 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7863 (mt-10) REVERT: F 253 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8222 (tppt) REVERT: I 218 MET cc_start: 0.8811 (tpp) cc_final: 0.8439 (tpt) REVERT: I 238 LYS cc_start: 0.8339 (mttt) cc_final: 0.8079 (mtpp) REVERT: I 253 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7480 (mmmt) REVERT: I 296 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8330 (mm-30) REVERT: J 218 MET cc_start: 0.8929 (tpp) cc_final: 0.8435 (tpt) REVERT: J 296 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7427 (tm-30) outliers start: 4 outliers final: 3 residues processed: 366 average time/residue: 0.6200 time to fit residues: 276.0621 Evaluate side-chains 262 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain I residue 162 TYR Chi-restraints excluded: chain I residue 258 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN J 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7385 Z= 0.252 Angle : 0.653 6.164 9980 Z= 0.355 Chirality : 0.038 0.138 1105 Planarity : 0.006 0.042 1295 Dihedral : 6.194 56.523 991 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.57 % Favored : 98.31 % Rotamer: Outliers : 2.69 % Allowed : 10.64 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 890 helix: 0.55 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -0.17 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 184 HIS 0.002 0.001 HIS D 219 PHE 0.014 0.002 PHE A 181 TYR 0.010 0.001 TYR J 254 ARG 0.005 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 256 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8363 (m-30) cc_final: 0.8069 (m-30) REVERT: A 286 PRO cc_start: 0.8531 (Cg_exo) cc_final: 0.8327 (Cg_endo) REVERT: D 253 LYS cc_start: 0.8396 (mtpt) cc_final: 0.8000 (mptt) REVERT: D 268 TYR cc_start: 0.8139 (t80) cc_final: 0.7393 (t80) REVERT: D 291 ASP cc_start: 0.7697 (m-30) cc_final: 0.7486 (m-30) REVERT: D 292 GLN cc_start: 0.8865 (mt0) cc_final: 0.8532 (mp10) REVERT: D 299 MET cc_start: 0.8148 (mtp) cc_final: 0.7930 (mtp) REVERT: D 306 ASN cc_start: 0.6302 (p0) cc_final: 0.6074 (p0) REVERT: F 232 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7879 (mt-10) REVERT: F 253 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8163 (tppt) REVERT: F 292 GLN cc_start: 0.8474 (mt0) cc_final: 0.8245 (tp-100) REVERT: F 328 MET cc_start: 0.6298 (mmm) cc_final: 0.6027 (mmm) REVERT: I 179 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7986 (mm-30) REVERT: I 218 MET cc_start: 0.8822 (tpp) cc_final: 0.8498 (tpt) REVERT: I 238 LYS cc_start: 0.8562 (mttt) cc_final: 0.8270 (mtpp) REVERT: J 179 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7456 (mm-30) REVERT: J 186 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8220 (tp30) REVERT: J 218 MET cc_start: 0.8956 (tpp) cc_final: 0.8431 (tpt) REVERT: J 254 TYR cc_start: 0.8477 (t80) cc_final: 0.8275 (t80) REVERT: J 296 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7563 (tm-30) REVERT: J 315 LEU cc_start: 0.7161 (mt) cc_final: 0.6712 (tp) outliers start: 21 outliers final: 16 residues processed: 263 average time/residue: 0.5416 time to fit residues: 178.2300 Evaluate side-chains 239 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 223 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain J residue 239 GLN Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 317 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN D 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7385 Z= 0.236 Angle : 0.585 6.057 9980 Z= 0.315 Chirality : 0.037 0.154 1105 Planarity : 0.005 0.042 1295 Dihedral : 5.519 55.211 989 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.13 % Favored : 97.64 % Rotamer: Outliers : 2.56 % Allowed : 12.82 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 890 helix: 0.80 (0.20), residues: 614 sheet: None (None), residues: 0 loop : -0.01 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 184 HIS 0.001 0.001 HIS D 219 PHE 0.014 0.001 PHE A 181 TYR 0.009 0.001 TYR D 268 ARG 0.008 0.001 ARG D 311 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 235 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8392 (m-30) cc_final: 0.8025 (m-30) REVERT: D 235 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6437 (mm-30) REVERT: D 253 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8000 (mptt) REVERT: D 268 TYR cc_start: 0.8173 (t80) cc_final: 0.7627 (t80) REVERT: D 292 GLN cc_start: 0.8748 (mt0) cc_final: 0.8427 (mp10) REVERT: D 306 ASN cc_start: 0.6316 (p0) cc_final: 0.5945 (p0) REVERT: F 253 LYS cc_start: 0.8379 (mtpt) cc_final: 0.8112 (tppt) REVERT: F 328 MET cc_start: 0.6411 (mmm) cc_final: 0.6181 (mmm) REVERT: I 238 LYS cc_start: 0.8615 (mttt) cc_final: 0.8333 (mtpp) REVERT: J 179 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7370 (mm-30) REVERT: J 218 MET cc_start: 0.8926 (tpp) cc_final: 0.8378 (tpt) REVERT: J 296 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7494 (tm-30) REVERT: J 315 LEU cc_start: 0.7098 (mt) cc_final: 0.6686 (tp) outliers start: 20 outliers final: 17 residues processed: 239 average time/residue: 0.5604 time to fit residues: 170.2027 Evaluate side-chains 240 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 223 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 239 GLN Chi-restraints excluded: chain J residue 295 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7385 Z= 0.206 Angle : 0.565 6.132 9980 Z= 0.297 Chirality : 0.036 0.144 1105 Planarity : 0.005 0.080 1295 Dihedral : 5.215 54.190 989 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.57 % Favored : 98.20 % Rotamer: Outliers : 2.82 % Allowed : 12.69 % Favored : 84.49 % 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: 1.04 (0.27), residues: 890 helix: 1.04 (0.20), residues: 614 sheet: None (None), residues: 0 loop : 0.11 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 184 HIS 0.001 0.000 HIS J 219 PHE 0.012 0.001 PHE A 181 TYR 0.010 0.001 TYR D 162 ARG 0.006 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 231 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8379 (m-30) cc_final: 0.8020 (m-30) REVERT: A 286 PRO cc_start: 0.8455 (Cg_exo) cc_final: 0.8175 (Cg_endo) REVERT: A 328 MET cc_start: 0.8071 (tpt) cc_final: 0.7616 (tpt) REVERT: D 253 LYS cc_start: 0.8446 (mtpt) cc_final: 0.7996 (mptt) REVERT: D 268 TYR cc_start: 0.8112 (t80) cc_final: 0.7494 (t80) REVERT: D 272 LEU cc_start: 0.8849 (tt) cc_final: 0.8516 (tp) REVERT: D 292 GLN cc_start: 0.8726 (mt0) cc_final: 0.8352 (mp10) REVERT: D 306 ASN cc_start: 0.6317 (p0) cc_final: 0.5923 (p0) REVERT: F 216 ASP cc_start: 0.8260 (m-30) cc_final: 0.8033 (m-30) REVERT: F 253 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8110 (tppt) REVERT: I 208 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8074 (mm-30) REVERT: I 238 LYS cc_start: 0.8618 (mttt) cc_final: 0.8342 (mtpp) REVERT: I 253 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7581 (tppt) REVERT: I 311 ARG cc_start: 0.9004 (mtp85) cc_final: 0.8124 (ttm110) REVERT: J 185 LEU cc_start: 0.9105 (tt) cc_final: 0.8876 (tt) REVERT: J 186 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8065 (tp30) REVERT: J 218 MET cc_start: 0.8897 (tpp) cc_final: 0.8378 (tpt) REVERT: J 254 TYR cc_start: 0.8505 (t80) cc_final: 0.7952 (t80) REVERT: J 296 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7459 (tm-30) REVERT: J 315 LEU cc_start: 0.7069 (mt) cc_final: 0.6669 (tp) outliers start: 22 outliers final: 16 residues processed: 237 average time/residue: 0.5262 time to fit residues: 156.9334 Evaluate side-chains 227 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 211 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 239 GLN Chi-restraints excluded: chain J residue 308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 7385 Z= 0.354 Angle : 0.612 6.116 9980 Z= 0.329 Chirality : 0.038 0.142 1105 Planarity : 0.005 0.051 1295 Dihedral : 5.209 53.169 989 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.70 % Favored : 97.19 % Rotamer: Outliers : 3.46 % Allowed : 14.10 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 890 helix: 0.94 (0.20), residues: 610 sheet: None (None), residues: 0 loop : -0.03 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 184 HIS 0.001 0.001 HIS I 219 PHE 0.020 0.002 PHE A 181 TYR 0.009 0.001 TYR D 268 ARG 0.005 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8435 (m-30) cc_final: 0.8056 (m-30) REVERT: A 222 GLN cc_start: 0.8219 (mt0) cc_final: 0.8005 (mt0) REVERT: D 253 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8126 (mptt) REVERT: D 268 TYR cc_start: 0.8132 (t80) cc_final: 0.7514 (t80) REVERT: D 292 GLN cc_start: 0.8736 (mt0) cc_final: 0.8242 (mm-40) REVERT: F 253 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8150 (tppt) REVERT: I 238 LYS cc_start: 0.8698 (mttt) cc_final: 0.8418 (mtpp) REVERT: I 253 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7712 (tppt) REVERT: I 311 ARG cc_start: 0.9024 (mtp85) cc_final: 0.8106 (ttm110) REVERT: J 179 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7429 (mm-30) REVERT: J 185 LEU cc_start: 0.9166 (tt) cc_final: 0.8941 (tt) REVERT: J 218 MET cc_start: 0.8888 (tpp) cc_final: 0.8470 (tpt) REVERT: J 315 LEU cc_start: 0.7031 (mt) cc_final: 0.6623 (tp) outliers start: 27 outliers final: 24 residues processed: 234 average time/residue: 0.5327 time to fit residues: 156.1327 Evaluate side-chains 236 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 239 GLN Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7385 Z= 0.258 Angle : 0.579 6.110 9980 Z= 0.306 Chirality : 0.036 0.144 1105 Planarity : 0.005 0.040 1295 Dihedral : 5.079 52.355 989 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.13 % Favored : 97.64 % Rotamer: Outliers : 2.82 % Allowed : 16.03 % Favored : 81.15 % 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: 1.06 (0.27), residues: 890 helix: 1.03 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.18 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 184 HIS 0.001 0.000 HIS J 219 PHE 0.014 0.001 PHE A 181 TYR 0.010 0.001 TYR D 162 ARG 0.004 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8394 (m-30) cc_final: 0.8001 (m-30) REVERT: A 222 GLN cc_start: 0.8174 (mt0) cc_final: 0.7967 (mt0) REVERT: A 328 MET cc_start: 0.8132 (tpt) cc_final: 0.7704 (tpt) REVERT: D 253 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8008 (mptt) REVERT: D 268 TYR cc_start: 0.8096 (t80) cc_final: 0.7459 (t80) REVERT: D 292 GLN cc_start: 0.8704 (mt0) cc_final: 0.8218 (mm-40) REVERT: F 194 GLU cc_start: 0.8155 (mp0) cc_final: 0.7924 (mp0) REVERT: F 253 LYS cc_start: 0.8402 (mtpt) cc_final: 0.8123 (tppt) REVERT: I 238 LYS cc_start: 0.8681 (mttt) cc_final: 0.8410 (mtpp) REVERT: I 253 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7691 (tppt) REVERT: I 296 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8595 (mm-30) REVERT: J 185 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8890 (tt) REVERT: J 218 MET cc_start: 0.8879 (tpp) cc_final: 0.8433 (tpt) REVERT: J 315 LEU cc_start: 0.7003 (mt) cc_final: 0.6661 (tp) outliers start: 22 outliers final: 17 residues processed: 228 average time/residue: 0.5616 time to fit residues: 162.5112 Evaluate side-chains 230 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7385 Z= 0.213 Angle : 0.569 8.480 9980 Z= 0.295 Chirality : 0.036 0.144 1105 Planarity : 0.005 0.038 1295 Dihedral : 4.627 22.383 987 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.47 % Favored : 97.30 % Rotamer: Outliers : 3.08 % Allowed : 16.67 % Favored : 80.26 % 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: 1.23 (0.28), residues: 890 helix: 1.15 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.29 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 184 HIS 0.001 0.000 HIS D 219 PHE 0.012 0.001 PHE A 181 TYR 0.010 0.001 TYR D 162 ARG 0.003 0.000 ARG I 311 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8370 (m-30) cc_final: 0.7974 (m-30) REVERT: A 328 MET cc_start: 0.8087 (tpt) cc_final: 0.7728 (tpt) REVERT: D 247 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7497 (ttm110) REVERT: D 253 LYS cc_start: 0.8486 (mtpt) cc_final: 0.7993 (mptt) REVERT: D 292 GLN cc_start: 0.8650 (mt0) cc_final: 0.8128 (mm-40) REVERT: D 326 GLN cc_start: 0.8509 (mt0) cc_final: 0.8297 (mt0) REVERT: F 194 GLU cc_start: 0.8156 (mp0) cc_final: 0.7920 (mp0) REVERT: F 253 LYS cc_start: 0.8382 (mtpt) cc_final: 0.8114 (tppt) REVERT: I 238 LYS cc_start: 0.8676 (mttt) cc_final: 0.8404 (mtpp) REVERT: I 249 THR cc_start: 0.7921 (m) cc_final: 0.7643 (p) REVERT: I 253 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7672 (tppt) REVERT: J 185 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8864 (tt) REVERT: J 218 MET cc_start: 0.8860 (tpp) cc_final: 0.8412 (tpt) REVERT: J 296 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7488 (tm-30) REVERT: J 315 LEU cc_start: 0.7113 (mt) cc_final: 0.6756 (tp) outliers start: 24 outliers final: 21 residues processed: 220 average time/residue: 0.5356 time to fit residues: 147.7746 Evaluate side-chains 227 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 258 TYR Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.6594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7385 Z= 0.269 Angle : 0.584 7.272 9980 Z= 0.307 Chirality : 0.036 0.144 1105 Planarity : 0.005 0.034 1295 Dihedral : 4.605 22.683 987 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.70 % Favored : 97.19 % Rotamer: Outliers : 3.08 % Allowed : 16.79 % Favored : 80.13 % 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: 1.18 (0.28), residues: 890 helix: 1.13 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.22 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 184 HIS 0.001 0.000 HIS I 219 PHE 0.015 0.001 PHE A 181 TYR 0.008 0.001 TYR D 162 ARG 0.003 0.000 ARG I 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8395 (m-30) cc_final: 0.8002 (m-30) REVERT: A 222 GLN cc_start: 0.8134 (mt0) cc_final: 0.7930 (mt0) REVERT: A 328 MET cc_start: 0.8109 (tpt) cc_final: 0.7714 (tpt) REVERT: D 247 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7587 (ttm110) REVERT: D 253 LYS cc_start: 0.8484 (mtpt) cc_final: 0.7997 (mptt) REVERT: D 292 GLN cc_start: 0.8670 (mt0) cc_final: 0.8145 (mm-40) REVERT: F 253 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8111 (tppt) REVERT: I 238 LYS cc_start: 0.8681 (mttt) cc_final: 0.8416 (mtpp) REVERT: I 249 THR cc_start: 0.7990 (m) cc_final: 0.7688 (p) REVERT: I 253 LYS cc_start: 0.8111 (mtpt) cc_final: 0.7716 (tppt) REVERT: I 296 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8731 (mm-30) REVERT: J 185 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8884 (tt) REVERT: J 218 MET cc_start: 0.8875 (tpp) cc_final: 0.8430 (tpt) REVERT: J 315 LEU cc_start: 0.7075 (mt) cc_final: 0.6740 (tp) outliers start: 24 outliers final: 21 residues processed: 221 average time/residue: 0.5320 time to fit residues: 150.3693 Evaluate side-chains 229 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 GLN ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.6669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7385 Z= 0.221 Angle : 0.578 7.293 9980 Z= 0.299 Chirality : 0.036 0.144 1105 Planarity : 0.005 0.034 1295 Dihedral : 4.540 22.500 987 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.58 % Favored : 97.30 % Rotamer: Outliers : 3.08 % Allowed : 16.67 % Favored : 80.26 % 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: 1.29 (0.28), residues: 890 helix: 1.20 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.28 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.001 0.000 HIS J 219 PHE 0.012 0.001 PHE A 181 TYR 0.009 0.001 TYR D 162 ARG 0.004 0.000 ARG I 311 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8371 (m-30) cc_final: 0.7961 (m-30) REVERT: A 222 GLN cc_start: 0.8134 (mt0) cc_final: 0.7918 (mt0) REVERT: A 328 MET cc_start: 0.8089 (tpt) cc_final: 0.7732 (tpt) REVERT: D 239 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: D 247 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7568 (ttm110) REVERT: D 253 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8004 (mptt) REVERT: D 292 GLN cc_start: 0.8651 (mt0) cc_final: 0.8124 (mm-40) REVERT: F 253 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8107 (tppt) REVERT: I 238 LYS cc_start: 0.8672 (mttt) cc_final: 0.8411 (mtpp) REVERT: I 249 THR cc_start: 0.7905 (m) cc_final: 0.7639 (p) REVERT: I 253 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7697 (tppt) REVERT: J 185 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8858 (tt) REVERT: J 218 MET cc_start: 0.8879 (tpp) cc_final: 0.8407 (tpt) REVERT: J 315 LEU cc_start: 0.7096 (mt) cc_final: 0.6762 (tp) outliers start: 24 outliers final: 21 residues processed: 220 average time/residue: 0.4974 time to fit residues: 138.2067 Evaluate side-chains 225 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7385 Z= 0.193 Angle : 0.568 7.235 9980 Z= 0.294 Chirality : 0.036 0.143 1105 Planarity : 0.005 0.036 1295 Dihedral : 4.483 22.286 987 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.36 % Favored : 97.42 % Rotamer: Outliers : 3.08 % Allowed : 16.79 % Favored : 80.13 % 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: 1.37 (0.28), residues: 890 helix: 1.27 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.30 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.000 0.000 HIS I 219 PHE 0.010 0.001 PHE A 181 TYR 0.009 0.001 TYR D 162 ARG 0.004 0.000 ARG I 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8353 (m-30) cc_final: 0.7941 (m-30) REVERT: A 222 GLN cc_start: 0.8171 (mt0) cc_final: 0.7928 (mt0) REVERT: A 328 MET cc_start: 0.8063 (tpt) cc_final: 0.7713 (tpt) REVERT: D 247 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7572 (ttm110) REVERT: D 253 LYS cc_start: 0.8468 (mtpt) cc_final: 0.7984 (mptt) REVERT: D 272 LEU cc_start: 0.8867 (tt) cc_final: 0.8544 (tp) REVERT: D 292 GLN cc_start: 0.8613 (mt0) cc_final: 0.8081 (mm-40) REVERT: F 253 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8096 (tppt) REVERT: F 306 ASN cc_start: 0.6336 (m-40) cc_final: 0.5767 (t0) REVERT: I 238 LYS cc_start: 0.8646 (mttt) cc_final: 0.8386 (mtpp) REVERT: I 249 THR cc_start: 0.7888 (m) cc_final: 0.7634 (p) REVERT: I 253 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7683 (tppt) REVERT: I 254 TYR cc_start: 0.8031 (t80) cc_final: 0.6777 (t80) REVERT: J 185 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8855 (tt) REVERT: J 218 MET cc_start: 0.8872 (tpp) cc_final: 0.8404 (tpt) REVERT: J 296 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7486 (tm-30) REVERT: J 315 LEU cc_start: 0.7068 (mt) cc_final: 0.6752 (tp) outliers start: 24 outliers final: 20 residues processed: 222 average time/residue: 0.5273 time to fit residues: 148.7017 Evaluate side-chains 229 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.141198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.113947 restraints weight = 37877.568| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 4.18 r_work: 0.3418 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7385 Z= 0.180 Angle : 0.565 7.180 9980 Z= 0.290 Chirality : 0.036 0.143 1105 Planarity : 0.005 0.056 1295 Dihedral : 4.396 22.240 987 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.25 % Favored : 97.64 % Rotamer: Outliers : 2.31 % Allowed : 17.69 % Favored : 80.00 % 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: 1.45 (0.28), residues: 890 helix: 1.34 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.31 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 205 HIS 0.000 0.000 HIS I 219 PHE 0.009 0.001 PHE A 181 TYR 0.009 0.001 TYR D 162 ARG 0.008 0.000 ARG D 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4161.23 seconds wall clock time: 73 minutes 0.71 seconds (4380.71 seconds total)