Starting phenix.real_space_refine on Sun Jan 19 22:42:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rb4_19025/01_2025/8rb4_19025.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rb4_19025/01_2025/8rb4_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/cci-nas-00/data/ceres_data/8rb4_19025/01_2025/8rb4_19025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rb4_19025/01_2025/8rb4_19025.map" model { file = "/net/cci-nas-00/data/ceres_data/8rb4_19025/01_2025/8rb4_19025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rb4_19025/01_2025/8rb4_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. Time to flip 71 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 7.54, per 1000 atoms: 0.52 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 - 3.00 Amino acid : True - 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: 3.75 Conformation dependent library (CDL) restraints added in 1.3 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: 1.01 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: 4.98 Time building geometry restraints manager: 4.49 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: 0.00 - 2.62: 22659 2.62 - 5.24: 3181 5.24 - 7.86: 882 7.86 - 10.48: 66 10.48 - 13.10: 17 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: 0.02 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: 0.770 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.710 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 4 poor density : 364 time to evaluate : 1.288 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: 0.6554 time to fit residues: 291.9258 Evaluate side-chains 262 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.142623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115807 restraints weight = 37474.604| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 4.13 r_work: 0.3397 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 to be fit. rotamer outliers: 21 poor density : 256 time to evaluate : 1.151 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 201 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7060 (mm-30) REVERT: A 216 ASP cc_start: 0.8813 (m-30) cc_final: 0.8545 (m-30) REVERT: A 283 ARG cc_start: 0.8879 (mtt180) cc_final: 0.8519 (mtm-85) REVERT: A 286 PRO cc_start: 0.8497 (Cg_exo) cc_final: 0.8211 (Cg_endo) REVERT: D 253 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8129 (mptt) REVERT: D 268 TYR cc_start: 0.8341 (t80) cc_final: 0.7610 (t80) REVERT: D 291 ASP cc_start: 0.8182 (m-30) cc_final: 0.7889 (m-30) REVERT: D 292 GLN cc_start: 0.9137 (mt0) cc_final: 0.8648 (mp10) REVERT: F 177 GLU cc_start: 0.8559 (pm20) cc_final: 0.8273 (pt0) REVERT: F 179 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8324 (mm-30) REVERT: F 201 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8529 (mm-30) REVERT: F 232 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8788 (mt-10) REVERT: F 253 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8210 (tppt) REVERT: F 292 GLN cc_start: 0.8710 (mt0) cc_final: 0.8338 (tp-100) REVERT: F 328 MET cc_start: 0.6718 (mmm) cc_final: 0.6365 (mmm) REVERT: I 218 MET cc_start: 0.9118 (tpp) cc_final: 0.8872 (tpt) REVERT: I 238 LYS cc_start: 0.8853 (mttt) cc_final: 0.8469 (mtpp) REVERT: J 179 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7900 (mm-30) REVERT: J 186 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8696 (tp30) REVERT: J 218 MET cc_start: 0.9282 (tpp) cc_final: 0.8825 (tpt) REVERT: J 254 TYR cc_start: 0.8838 (t80) cc_final: 0.8618 (t80) REVERT: J 283 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8269 (ttp-110) REVERT: J 296 GLU cc_start: 0.8694 (mt-10) cc_final: 0.7631 (tm-30) REVERT: J 315 LEU cc_start: 0.7444 (mt) cc_final: 0.6971 (tp) outliers start: 21 outliers final: 16 residues processed: 263 average time/residue: 0.5699 time to fit residues: 187.3422 Evaluate side-chains 239 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 27 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 34 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.140457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112433 restraints weight = 37553.032| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 4.22 r_work: 0.3386 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5454 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= 0.224 Angle : 0.581 6.027 9980 Z= 0.311 Chirality : 0.037 0.154 1105 Planarity : 0.005 0.045 1295 Dihedral : 5.516 55.229 989 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.13 % Favored : 97.64 % Rotamer: Outliers : 2.44 % Allowed : 12.95 % 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: 0.75 (0.27), residues: 890 helix: 0.82 (0.20), residues: 614 sheet: None (None), residues: 0 loop : 0.00 (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 0.013 0.001 PHE A 181 TYR 0.009 0.001 TYR D 162 ARG 0.009 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 252 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 1.212 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 201 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7008 (mm-30) REVERT: A 216 ASP cc_start: 0.8798 (m-30) cc_final: 0.8472 (m-30) REVERT: A 283 ARG cc_start: 0.8830 (mtt180) cc_final: 0.8595 (mmm-85) REVERT: A 328 MET cc_start: 0.8178 (tpt) cc_final: 0.7630 (tpt) REVERT: D 235 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7687 (mm-30) REVERT: D 253 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8126 (mptt) REVERT: D 268 TYR cc_start: 0.8363 (t80) cc_final: 0.7821 (t80) REVERT: D 291 ASP cc_start: 0.8290 (m-30) cc_final: 0.8037 (m-30) REVERT: D 292 GLN cc_start: 0.9042 (mt0) cc_final: 0.8562 (mp10) REVERT: F 201 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8509 (mm-30) REVERT: F 253 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8192 (tppt) REVERT: F 292 GLN cc_start: 0.8647 (mt0) cc_final: 0.8342 (tp-100) REVERT: F 328 MET cc_start: 0.6792 (mmm) cc_final: 0.6502 (mmm) REVERT: I 164 LYS cc_start: 0.9149 (mttp) cc_final: 0.8904 (mtpt) REVERT: I 238 LYS cc_start: 0.8886 (mttt) cc_final: 0.8513 (mtpp) REVERT: J 179 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8010 (mm-30) REVERT: J 218 MET cc_start: 0.9288 (tpp) cc_final: 0.8832 (tpt) REVERT: J 283 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8210 (ttp-110) REVERT: J 296 GLU cc_start: 0.8633 (mt-10) cc_final: 0.7540 (tm-30) REVERT: J 315 LEU cc_start: 0.7355 (mt) cc_final: 0.6916 (tp) outliers start: 19 outliers final: 16 residues processed: 238 average time/residue: 0.5565 time to fit residues: 166.2773 Evaluate side-chains 242 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.140387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.112786 restraints weight = 37286.067| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.18 r_work: 0.3395 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7385 Z= 0.200 Angle : 0.558 6.117 9980 Z= 0.293 Chirality : 0.036 0.145 1105 Planarity : 0.005 0.074 1295 Dihedral : 5.201 54.267 989 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.57 % Favored : 98.20 % Rotamer: Outliers : 2.95 % Allowed : 12.56 % 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: 1.06 (0.27), residues: 890 helix: 1.06 (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 A 184 HIS 0.001 0.000 HIS I 219 PHE 0.011 0.001 PHE A 181 TYR 0.009 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 251 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 1.090 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 201 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7002 (mm-30) REVERT: A 216 ASP cc_start: 0.8747 (m-30) cc_final: 0.8420 (m-30) REVERT: A 286 PRO cc_start: 0.8445 (Cg_exo) cc_final: 0.8123 (Cg_endo) REVERT: A 328 MET cc_start: 0.8200 (tpt) cc_final: 0.7724 (tpt) REVERT: D 253 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8123 (mptt) REVERT: D 268 TYR cc_start: 0.8264 (t80) cc_final: 0.7708 (t80) REVERT: D 272 LEU cc_start: 0.9050 (tt) cc_final: 0.8716 (tp) REVERT: D 291 ASP cc_start: 0.8201 (m-30) cc_final: 0.7983 (m-30) REVERT: D 292 GLN cc_start: 0.8981 (mt0) cc_final: 0.8488 (mp10) REVERT: D 306 ASN cc_start: 0.7065 (p0) cc_final: 0.6854 (p0) REVERT: F 164 LYS cc_start: 0.8630 (tptt) cc_final: 0.8241 (ttpp) REVERT: F 201 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8494 (mm-30) REVERT: F 253 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8192 (tppt) REVERT: F 292 GLN cc_start: 0.8639 (mt0) cc_final: 0.8297 (tp-100) REVERT: F 328 MET cc_start: 0.6814 (mmm) cc_final: 0.6547 (mmm) REVERT: I 164 LYS cc_start: 0.9073 (mttp) cc_final: 0.8838 (mtpt) REVERT: I 208 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8577 (mm-30) REVERT: I 235 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8787 (mm-30) REVERT: I 238 LYS cc_start: 0.8900 (mttt) cc_final: 0.8516 (mtpp) REVERT: I 253 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7697 (tppt) REVERT: I 311 ARG cc_start: 0.9142 (mtp85) cc_final: 0.8255 (ttm110) REVERT: J 185 LEU cc_start: 0.9236 (tt) cc_final: 0.8998 (tt) REVERT: J 186 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8577 (tp30) REVERT: J 218 MET cc_start: 0.9256 (tpp) cc_final: 0.8803 (tpt) REVERT: J 254 TYR cc_start: 0.8847 (t80) cc_final: 0.8171 (t80) REVERT: J 283 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8211 (ttp-110) REVERT: J 296 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7510 (tm-30) REVERT: J 315 LEU cc_start: 0.7341 (mt) cc_final: 0.6917 (tp) outliers start: 23 outliers final: 16 residues processed: 235 average time/residue: 0.5555 time to fit residues: 164.4922 Evaluate side-chains 230 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 191 ILE 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 30 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.139667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.112436 restraints weight = 37908.023| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.18 r_work: 0.3366 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7385 Z= 0.270 Angle : 0.571 6.121 9980 Z= 0.304 Chirality : 0.037 0.141 1105 Planarity : 0.005 0.054 1295 Dihedral : 5.069 53.309 989 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.13 % Favored : 97.64 % Rotamer: Outliers : 3.33 % Allowed : 14.23 % 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: 1.06 (0.27), residues: 890 helix: 1.07 (0.20), residues: 612 sheet: None (None), residues: 0 loop : 0.09 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 184 HIS 0.001 0.000 HIS I 219 PHE 0.017 0.002 PHE A 181 TYR 0.009 0.001 TYR D 162 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 249 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 1.170 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 201 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7026 (mm-30) REVERT: A 216 ASP cc_start: 0.8806 (m-30) cc_final: 0.8463 (m-30) REVERT: A 222 GLN cc_start: 0.8569 (mt0) cc_final: 0.8361 (mt0) REVERT: A 286 PRO cc_start: 0.8522 (Cg_exo) cc_final: 0.8278 (Cg_endo) REVERT: A 328 MET cc_start: 0.8255 (tpt) cc_final: 0.7784 (tpt) REVERT: D 253 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8160 (mptt) REVERT: D 264 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7864 (mtpt) REVERT: D 268 TYR cc_start: 0.8282 (t80) cc_final: 0.7745 (t80) REVERT: D 272 LEU cc_start: 0.9085 (tt) cc_final: 0.8734 (tp) REVERT: D 291 ASP cc_start: 0.8210 (m-30) cc_final: 0.7875 (m-30) REVERT: D 292 GLN cc_start: 0.9002 (mt0) cc_final: 0.8395 (mm-40) REVERT: F 201 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8466 (mm-30) REVERT: F 253 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8216 (tppt) REVERT: F 283 ARG cc_start: 0.8554 (mtm110) cc_final: 0.8324 (ttm-80) REVERT: F 292 GLN cc_start: 0.8676 (mt0) cc_final: 0.8363 (tp-100) REVERT: I 164 LYS cc_start: 0.9075 (mttp) cc_final: 0.8827 (mtpt) REVERT: I 208 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8539 (mm-30) REVERT: I 235 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8811 (mm-30) REVERT: I 238 LYS cc_start: 0.8925 (mttt) cc_final: 0.8546 (mtpp) REVERT: I 253 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7794 (tppt) REVERT: I 296 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8823 (mm-30) REVERT: J 185 LEU cc_start: 0.9277 (tt) cc_final: 0.9021 (tt) REVERT: J 218 MET cc_start: 0.9253 (tpp) cc_final: 0.8870 (tpt) REVERT: J 283 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8167 (ttp-110) REVERT: J 296 GLU cc_start: 0.8627 (mt-10) cc_final: 0.7594 (tm-30) REVERT: J 315 LEU cc_start: 0.7345 (mt) cc_final: 0.6923 (tp) outliers start: 26 outliers final: 21 residues processed: 233 average time/residue: 0.5476 time to fit residues: 160.8454 Evaluate side-chains 235 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 I residue 171 SER Chi-restraints excluded: chain I residue 191 ILE 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 266 SER 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 62 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.140216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112325 restraints weight = 37928.294| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 4.26 r_work: 0.3384 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6272 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= 0.209 Angle : 0.562 8.328 9980 Z= 0.291 Chirality : 0.036 0.144 1105 Planarity : 0.005 0.042 1295 Dihedral : 4.915 52.387 989 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.02 % Favored : 97.75 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % Favored : 82.05 % 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: 1.22 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.25 (0.37), 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 0.013 0.001 PHE A 181 TYR 0.009 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 237 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 1.281 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 201 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7021 (mm-30) REVERT: A 216 ASP cc_start: 0.8763 (m-30) cc_final: 0.8409 (m-30) REVERT: A 222 GLN cc_start: 0.8570 (mt0) cc_final: 0.8308 (mt0) REVERT: A 286 PRO cc_start: 0.8532 (Cg_exo) cc_final: 0.8283 (Cg_endo) REVERT: A 328 MET cc_start: 0.8257 (tpt) cc_final: 0.7830 (tpt) REVERT: D 247 ARG cc_start: 0.8123 (ttm110) cc_final: 0.7815 (ttm110) REVERT: D 253 LYS cc_start: 0.8616 (mtpt) cc_final: 0.8143 (mptt) REVERT: D 272 LEU cc_start: 0.9083 (tt) cc_final: 0.8755 (tp) REVERT: D 291 ASP cc_start: 0.8158 (m-30) cc_final: 0.7829 (m-30) REVERT: D 292 GLN cc_start: 0.8981 (mt0) cc_final: 0.8374 (mm-40) REVERT: F 164 LYS cc_start: 0.8614 (tptt) cc_final: 0.8229 (ttpp) REVERT: F 194 GLU cc_start: 0.8481 (mp0) cc_final: 0.8158 (mp0) REVERT: F 201 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8399 (mm-30) REVERT: F 253 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8207 (tppt) REVERT: F 283 ARG cc_start: 0.8536 (mtm110) cc_final: 0.8320 (ttm-80) REVERT: F 292 GLN cc_start: 0.8647 (mt0) cc_final: 0.8313 (tp-100) REVERT: I 164 LYS cc_start: 0.9032 (mttp) cc_final: 0.8807 (mtpt) REVERT: I 235 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8797 (mm-30) REVERT: I 238 LYS cc_start: 0.8928 (mttt) cc_final: 0.8550 (mtpp) REVERT: I 253 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7777 (tppt) REVERT: J 185 LEU cc_start: 0.9256 (tt) cc_final: 0.8983 (tt) REVERT: J 218 MET cc_start: 0.9239 (tpp) cc_final: 0.8842 (tpt) REVERT: J 296 GLU cc_start: 0.8638 (mt-10) cc_final: 0.7559 (tm-30) REVERT: J 315 LEU cc_start: 0.7382 (mt) cc_final: 0.6994 (tp) outliers start: 20 outliers final: 18 residues processed: 226 average time/residue: 0.5571 time to fit residues: 158.8898 Evaluate side-chains 225 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 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 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 270 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 79 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.141353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113352 restraints weight = 37698.754| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 4.26 r_work: 0.3398 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.6405 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= 0.176 Angle : 0.538 7.340 9980 Z= 0.278 Chirality : 0.035 0.143 1105 Planarity : 0.004 0.035 1295 Dihedral : 4.455 21.379 987 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.13 % Favored : 97.64 % Rotamer: Outliers : 2.44 % Allowed : 16.15 % Favored : 81.41 % 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: 1.48 (0.28), residues: 890 helix: 1.35 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.35 (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 0.010 0.001 PHE A 181 TYR 0.009 0.001 TYR D 162 ARG 0.002 0.000 ARG A 211 *********************** 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 238 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 1.127 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: A 201 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7038 (mm-30) REVERT: A 216 ASP cc_start: 0.8767 (m-30) cc_final: 0.8419 (m-30) REVERT: A 222 GLN cc_start: 0.8612 (mt0) cc_final: 0.8339 (mt0) REVERT: A 286 PRO cc_start: 0.8525 (Cg_exo) cc_final: 0.8268 (Cg_endo) REVERT: A 328 MET cc_start: 0.8180 (tpt) cc_final: 0.7809 (tpt) REVERT: D 247 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7834 (ttm110) REVERT: D 253 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8121 (mptt) REVERT: D 256 ARG cc_start: 0.7683 (tpp-160) cc_final: 0.7465 (tpp-160) REVERT: D 291 ASP cc_start: 0.8144 (m-30) cc_final: 0.7795 (m-30) REVERT: D 292 GLN cc_start: 0.8937 (mt0) cc_final: 0.8296 (mm-40) REVERT: D 306 ASN cc_start: 0.7078 (p0) cc_final: 0.6856 (p0) REVERT: D 326 GLN cc_start: 0.8723 (mt0) cc_final: 0.8495 (mt0) REVERT: F 164 LYS cc_start: 0.8598 (tptt) cc_final: 0.8233 (ttpp) REVERT: F 194 GLU cc_start: 0.8493 (mp0) cc_final: 0.8159 (mp0) REVERT: F 201 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8412 (mm-30) REVERT: F 253 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8197 (tppt) REVERT: F 283 ARG cc_start: 0.8556 (mtm110) cc_final: 0.8306 (ttm-80) REVERT: F 292 GLN cc_start: 0.8622 (mt0) cc_final: 0.8302 (tp-100) REVERT: F 306 ASN cc_start: 0.6329 (m-40) cc_final: 0.5743 (t0) REVERT: F 315 LEU cc_start: 0.8094 (mt) cc_final: 0.7748 (mt) REVERT: I 164 LYS cc_start: 0.9005 (mttp) cc_final: 0.8795 (mtpt) REVERT: I 194 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8568 (mp0) REVERT: I 235 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8771 (mm-30) REVERT: I 238 LYS cc_start: 0.8914 (mttt) cc_final: 0.8542 (mtpp) REVERT: I 249 THR cc_start: 0.8131 (m) cc_final: 0.7868 (p) REVERT: I 253 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7747 (tppt) REVERT: I 311 ARG cc_start: 0.9145 (mtp85) cc_final: 0.8259 (ttm110) REVERT: J 185 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8930 (tt) REVERT: J 218 MET cc_start: 0.9228 (tpp) cc_final: 0.8840 (tpt) REVERT: J 296 GLU cc_start: 0.8624 (mt-10) cc_final: 0.7563 (tm-30) REVERT: J 315 LEU cc_start: 0.7389 (mt) cc_final: 0.7024 (tp) outliers start: 19 outliers final: 17 residues processed: 226 average time/residue: 0.5450 time to fit residues: 155.5497 Evaluate side-chains 228 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 F residue 167 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 314 GLU 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 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 89 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.0020 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.143355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.116033 restraints weight = 37365.295| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.15 r_work: 0.3442 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7385 Z= 0.152 Angle : 0.523 7.102 9980 Z= 0.268 Chirality : 0.035 0.142 1105 Planarity : 0.004 0.033 1295 Dihedral : 4.263 20.863 987 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.02 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 17.05 % Favored : 81.03 % 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: 1.65 (0.28), residues: 890 helix: 1.48 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.41 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.001 0.000 HIS F 219 PHE 0.007 0.001 PHE F 181 TYR 0.009 0.001 TYR D 162 ARG 0.003 0.000 ARG A 211 *********************** 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 236 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 221 time to evaluate : 1.191 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 201 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7030 (mm-30) REVERT: A 216 ASP cc_start: 0.8755 (m-30) cc_final: 0.8417 (m-30) REVERT: A 263 GLU cc_start: 0.7638 (tt0) cc_final: 0.7419 (tt0) REVERT: A 286 PRO cc_start: 0.8484 (Cg_exo) cc_final: 0.8213 (Cg_endo) REVERT: A 328 MET cc_start: 0.8139 (tpt) cc_final: 0.7816 (tpt) REVERT: D 239 GLN cc_start: 0.8471 (mt0) cc_final: 0.7953 (mp10) REVERT: D 247 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7844 (ttm110) REVERT: D 253 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8114 (mptt) REVERT: D 256 ARG cc_start: 0.7690 (tpp-160) cc_final: 0.7482 (tpp-160) REVERT: D 291 ASP cc_start: 0.8101 (m-30) cc_final: 0.7765 (m-30) REVERT: D 292 GLN cc_start: 0.8817 (mt0) cc_final: 0.8193 (mm-40) REVERT: D 306 ASN cc_start: 0.6973 (p0) cc_final: 0.6764 (p0) REVERT: F 164 LYS cc_start: 0.8568 (tptt) cc_final: 0.8218 (ttpp) REVERT: F 194 GLU cc_start: 0.8517 (mp0) cc_final: 0.8176 (mp0) REVERT: F 201 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8400 (mm-30) REVERT: F 253 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8178 (tppt) REVERT: F 256 ARG cc_start: 0.7506 (mmt-90) cc_final: 0.7130 (mmt-90) REVERT: F 283 ARG cc_start: 0.8558 (mtm110) cc_final: 0.8353 (ttm-80) REVERT: F 292 GLN cc_start: 0.8611 (mt0) cc_final: 0.8282 (tp-100) REVERT: F 306 ASN cc_start: 0.6224 (m-40) cc_final: 0.5737 (t0) REVERT: I 194 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8570 (mp0) REVERT: I 235 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8765 (mm-30) REVERT: I 238 LYS cc_start: 0.8844 (mttt) cc_final: 0.8501 (mtpp) REVERT: I 249 THR cc_start: 0.8058 (m) cc_final: 0.7810 (p) REVERT: I 253 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7727 (tppt) REVERT: I 311 ARG cc_start: 0.9123 (mtp85) cc_final: 0.8210 (ttm110) REVERT: J 185 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8892 (tt) REVERT: J 218 MET cc_start: 0.9202 (tpp) cc_final: 0.8776 (tpt) REVERT: J 296 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7496 (tm-30) REVERT: J 315 LEU cc_start: 0.7392 (mt) cc_final: 0.7053 (tp) outliers start: 15 outliers final: 12 residues processed: 227 average time/residue: 0.5100 time to fit residues: 146.7424 Evaluate side-chains 231 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 243 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 270 LEU 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 0 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** D 259 GLN J 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.139528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111885 restraints weight = 37859.460| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 4.18 r_work: 0.3381 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6667 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= 0.284 Angle : 0.569 6.570 9980 Z= 0.302 Chirality : 0.037 0.143 1105 Planarity : 0.005 0.043 1295 Dihedral : 4.372 21.988 987 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.47 % Favored : 97.30 % Rotamer: Outliers : 2.18 % Allowed : 17.05 % Favored : 80.77 % 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: 1.33 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 0.34 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 184 HIS 0.001 0.000 HIS I 219 PHE 0.017 0.002 PHE A 181 TYR 0.008 0.001 TYR D 268 ARG 0.002 0.000 ARG A 166 *********************** 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 235 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 1.132 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 201 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 216 ASP cc_start: 0.8839 (m-30) cc_final: 0.8500 (m-30) REVERT: A 286 PRO cc_start: 0.8580 (Cg_exo) cc_final: 0.8336 (Cg_endo) REVERT: A 328 MET cc_start: 0.8198 (tpt) cc_final: 0.7818 (tpt) REVERT: D 225 ASN cc_start: 0.7675 (t0) cc_final: 0.7393 (t0) REVERT: D 239 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: D 247 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7997 (ttm110) REVERT: D 253 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8424 (tptt) REVERT: D 272 LEU cc_start: 0.9096 (tt) cc_final: 0.8778 (tp) REVERT: D 291 ASP cc_start: 0.8171 (m-30) cc_final: 0.7828 (m-30) REVERT: D 292 GLN cc_start: 0.8879 (mt0) cc_final: 0.8233 (mm-40) REVERT: D 326 GLN cc_start: 0.8720 (mt0) cc_final: 0.8489 (mt0) REVERT: F 164 LYS cc_start: 0.8746 (tptt) cc_final: 0.8401 (ttpp) REVERT: F 194 GLU cc_start: 0.8599 (mp0) cc_final: 0.8255 (mp0) REVERT: F 201 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8435 (mm-30) REVERT: F 253 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8206 (tppt) REVERT: F 292 GLN cc_start: 0.8608 (mt0) cc_final: 0.8294 (tp-100) REVERT: F 306 ASN cc_start: 0.6288 (m-40) cc_final: 0.5667 (t0) REVERT: I 194 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8609 (mp0) REVERT: I 235 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8753 (mm-30) REVERT: I 238 LYS cc_start: 0.8916 (mttt) cc_final: 0.8577 (mtpp) REVERT: I 249 THR cc_start: 0.8134 (m) cc_final: 0.7871 (p) REVERT: I 253 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7837 (tppt) REVERT: I 311 ARG cc_start: 0.9149 (mtp85) cc_final: 0.8218 (ttm110) REVERT: J 185 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8990 (tt) REVERT: J 218 MET cc_start: 0.9210 (tpp) cc_final: 0.8849 (tpt) REVERT: J 315 LEU cc_start: 0.7454 (mt) cc_final: 0.7063 (tp) outliers start: 17 outliers final: 14 residues processed: 224 average time/residue: 0.5609 time to fit residues: 159.7094 Evaluate side-chains 226 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 239 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 F residue 243 SER Chi-restraints excluded: chain F residue 318 GLN 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 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 12 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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** A 292 GLN ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.141854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114271 restraints weight = 37776.404| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 4.22 r_work: 0.3428 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.6758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7385 Z= 0.185 Angle : 0.560 6.981 9980 Z= 0.289 Chirality : 0.036 0.143 1105 Planarity : 0.005 0.042 1295 Dihedral : 4.315 21.302 987 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.91 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 17.31 % Favored : 80.77 % 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 (0.28), residues: 890 helix: 1.43 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.36 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 184 HIS 0.001 0.000 HIS F 219 PHE 0.010 0.001 PHE A 181 TYR 0.009 0.001 TYR D 162 ARG 0.006 0.000 ARG I 332 ********************** 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 226 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 1.312 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 201 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7035 (mm-30) REVERT: A 216 ASP cc_start: 0.8782 (m-30) cc_final: 0.8431 (m-30) REVERT: A 286 PRO cc_start: 0.8518 (Cg_exo) cc_final: 0.8264 (Cg_endo) REVERT: A 328 MET cc_start: 0.8194 (tpt) cc_final: 0.7825 (tpt) REVERT: D 202 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8169 (mtpt) REVERT: D 239 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: D 247 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7927 (ttm110) REVERT: D 253 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8134 (mptt) REVERT: D 291 ASP cc_start: 0.8134 (m-30) cc_final: 0.7818 (m-30) REVERT: D 292 GLN cc_start: 0.8855 (mt0) cc_final: 0.8205 (mm-40) REVERT: D 326 GLN cc_start: 0.8691 (mt0) cc_final: 0.8471 (mt0) REVERT: F 164 LYS cc_start: 0.8634 (tptt) cc_final: 0.8316 (ttpp) REVERT: F 194 GLU cc_start: 0.8606 (mp0) cc_final: 0.8262 (mp0) REVERT: F 201 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8371 (mm-30) REVERT: F 253 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8174 (tppt) REVERT: F 256 ARG cc_start: 0.7603 (mmt-90) cc_final: 0.7233 (mmt-90) REVERT: F 292 GLN cc_start: 0.8570 (mt0) cc_final: 0.8263 (tp-100) REVERT: F 306 ASN cc_start: 0.6221 (m-40) cc_final: 0.5714 (t0) REVERT: I 194 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8550 (mp0) REVERT: I 235 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8758 (mm-30) REVERT: I 238 LYS cc_start: 0.8864 (mttt) cc_final: 0.8504 (mtpp) REVERT: I 249 THR cc_start: 0.8058 (m) cc_final: 0.7795 (p) REVERT: I 253 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7771 (tppt) REVERT: I 254 TYR cc_start: 0.8437 (t80) cc_final: 0.7173 (t80) REVERT: I 311 ARG cc_start: 0.9122 (mtp85) cc_final: 0.8199 (ttm110) REVERT: J 185 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8988 (tt) REVERT: J 218 MET cc_start: 0.9209 (tpp) cc_final: 0.8828 (tpt) REVERT: J 296 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7562 (tm-30) REVERT: J 315 LEU cc_start: 0.7478 (mt) cc_final: 0.7139 (tp) outliers start: 15 outliers final: 12 residues processed: 217 average time/residue: 0.5348 time to fit residues: 147.0283 Evaluate side-chains 223 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 239 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 F residue 243 SER Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 234 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.140832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.114136 restraints weight = 38030.303| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 4.09 r_work: 0.3421 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7385 Z= 0.212 Angle : 0.558 6.615 9980 Z= 0.289 Chirality : 0.036 0.143 1105 Planarity : 0.004 0.042 1295 Dihedral : 4.282 21.717 987 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.47 % Favored : 97.30 % Rotamer: Outliers : 1.79 % Allowed : 17.31 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.28), residues: 890 helix: 1.39 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.40 (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 A 219 PHE 0.013 0.001 PHE A 181 TYR 0.008 0.001 TYR D 162 ARG 0.002 0.000 ARG A 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7172.95 seconds wall clock time: 127 minutes 52.34 seconds (7672.34 seconds total)