Starting phenix.real_space_refine on Sat Oct 11 11:50:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rb4_19025/10_2025/8rb4_19025.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rb4_19025/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rb4_19025/10_2025/8rb4_19025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rb4_19025/10_2025/8rb4_19025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rb4_19025/10_2025/8rb4_19025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rb4_19025/10_2025/8rb4_19025.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.95, per 1000 atoms: 0.20 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: 1.32 Conformation dependent library (CDL) restraints added in 409.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.35 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: 2.96 Time building geometry restraints manager: 1.87 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.090 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.750 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- 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= 0.812 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG I 204 TYR 0.066 0.015 TYR I 258 PHE 0.052 0.014 PHE F 237 TRP 0.161 0.027 TRP A 205 HIS 0.008 0.004 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.01362 ( 7385) covalent geometry : angle 1.82539 ( 9980) hydrogen bonds : bond 0.16647 ( 435) hydrogen bonds : angle 7.28880 ( 1299) *********************** 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 : 0.416 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: 0.3164 time to fit residues: 139.9681 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 : 0.478 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.143804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116771 restraints weight = 37377.533| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 4.15 r_work: 0.3403 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7385 Z= 0.172 Angle : 0.648 6.155 9980 Z= 0.353 Chirality : 0.038 0.141 1105 Planarity : 0.006 0.044 1295 Dihedral : 6.128 56.482 991 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.46 % Favored : 98.43 % Rotamer: Outliers : 2.56 % Allowed : 10.51 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.26), residues: 890 helix: 0.60 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -0.12 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 247 TYR 0.009 0.001 TYR J 254 PHE 0.013 0.001 PHE A 181 TRP 0.016 0.002 TRP D 184 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 7385) covalent geometry : angle 0.64835 ( 9980) hydrogen bonds : bond 0.05632 ( 435) hydrogen bonds : angle 5.18111 ( 1299) *********************** 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 279 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 0.469 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: A 201 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7033 (mm-30) REVERT: A 216 ASP cc_start: 0.8790 (m-30) cc_final: 0.8503 (m-30) REVERT: A 283 ARG cc_start: 0.8879 (mtt180) cc_final: 0.8521 (mtm-85) REVERT: A 286 PRO cc_start: 0.8487 (Cg_exo) cc_final: 0.8198 (Cg_endo) REVERT: D 253 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8128 (mptt) REVERT: D 268 TYR cc_start: 0.8350 (t80) cc_final: 0.7689 (t80) REVERT: D 291 ASP cc_start: 0.8190 (m-30) cc_final: 0.7900 (m-30) REVERT: D 292 GLN cc_start: 0.9097 (mt0) cc_final: 0.8624 (mp10) REVERT: F 177 GLU cc_start: 0.8522 (pm20) cc_final: 0.8278 (pt0) REVERT: F 179 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8309 (mm-30) REVERT: F 232 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8780 (mt-10) REVERT: F 253 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8187 (tppt) REVERT: F 292 GLN cc_start: 0.8695 (mt0) cc_final: 0.8370 (tp-100) REVERT: F 328 MET cc_start: 0.6771 (mmm) cc_final: 0.6436 (tpt) REVERT: I 164 LYS cc_start: 0.9092 (mttp) cc_final: 0.8857 (mtpt) REVERT: I 218 MET cc_start: 0.9126 (tpp) cc_final: 0.8859 (tpt) REVERT: I 228 ILE cc_start: 0.8333 (tt) cc_final: 0.8063 (tt) REVERT: I 238 LYS cc_start: 0.8875 (mttt) cc_final: 0.8489 (mtpp) REVERT: J 179 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7917 (mm-30) REVERT: J 186 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8686 (tp30) REVERT: J 218 MET cc_start: 0.9282 (tpp) cc_final: 0.8824 (tpt) REVERT: J 254 TYR cc_start: 0.8837 (t80) cc_final: 0.8624 (t80) REVERT: J 283 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8222 (ttp-110) REVERT: J 292 GLN cc_start: 0.8999 (mt0) cc_final: 0.8726 (mm-40) REVERT: J 296 GLU cc_start: 0.8656 (mt-10) cc_final: 0.7811 (tm-30) REVERT: J 315 LEU cc_start: 0.7430 (mt) cc_final: 0.6962 (tp) outliers start: 20 outliers final: 15 residues processed: 267 average time/residue: 0.2650 time to fit residues: 88.2847 Evaluate side-chains 239 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 79 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.137448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110504 restraints weight = 37966.508| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 4.11 r_work: 0.3357 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7385 Z= 0.233 Angle : 0.628 6.081 9980 Z= 0.342 Chirality : 0.038 0.150 1105 Planarity : 0.005 0.046 1295 Dihedral : 5.607 55.225 989 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.58 % Favored : 97.19 % Rotamer: Outliers : 2.18 % Allowed : 13.72 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.27), residues: 890 helix: 0.69 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -0.12 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 311 TYR 0.010 0.002 TYR D 268 PHE 0.019 0.002 PHE A 181 TRP 0.011 0.002 TRP F 184 HIS 0.002 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 7385) covalent geometry : angle 0.62761 ( 9980) hydrogen bonds : bond 0.05234 ( 435) hydrogen bonds : angle 5.20973 ( 1299) *********************** 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: 17 poor density : 235 time to evaluate : 0.243 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: 0.7341 (mm-30) cc_final: 0.7035 (mm-30) REVERT: A 216 ASP cc_start: 0.8837 (m-30) cc_final: 0.8520 (m-30) REVERT: A 283 ARG cc_start: 0.8787 (mtt180) cc_final: 0.8584 (mmm-85) REVERT: A 328 MET cc_start: 0.8223 (tpt) cc_final: 0.7644 (tpt) REVERT: D 253 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8177 (mptt) REVERT: D 268 TYR cc_start: 0.8335 (t80) cc_final: 0.7795 (t80) REVERT: D 291 ASP cc_start: 0.8375 (m-30) cc_final: 0.8148 (m-30) REVERT: D 292 GLN cc_start: 0.9053 (mt0) cc_final: 0.8567 (mp10) REVERT: F 201 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8547 (mm-30) REVERT: F 253 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8203 (tppt) REVERT: F 292 GLN cc_start: 0.8675 (mt0) cc_final: 0.8365 (tp-100) REVERT: I 164 LYS cc_start: 0.9132 (mttp) cc_final: 0.8885 (mtpt) REVERT: I 238 LYS cc_start: 0.8907 (mttt) cc_final: 0.8545 (mtpp) REVERT: I 253 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7735 (tppt) REVERT: I 311 ARG cc_start: 0.9141 (mtp85) cc_final: 0.8247 (ttm110) REVERT: J 179 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8075 (mm-30) REVERT: J 218 MET cc_start: 0.9276 (tpp) cc_final: 0.8857 (tpt) REVERT: J 283 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8196 (ttp-110) REVERT: J 296 GLU cc_start: 0.8668 (mt-10) cc_final: 0.7620 (tm-30) REVERT: J 315 LEU cc_start: 0.7305 (mt) cc_final: 0.6855 (tp) outliers start: 17 outliers final: 16 residues processed: 239 average time/residue: 0.2546 time to fit residues: 76.2294 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 : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 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 158 LEU 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 295 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 42 optimal weight: 6.9990 chunk 56 optimal weight: 0.0170 chunk 89 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- 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 ** 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 = 0.3905 r_free = 0.3905 target = 0.141723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.115328 restraints weight = 37810.943| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 4.05 r_work: 0.3420 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5947 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= 0.129 Angle : 0.558 6.142 9980 Z= 0.293 Chirality : 0.036 0.144 1105 Planarity : 0.005 0.042 1295 Dihedral : 5.231 53.804 989 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.91 % Favored : 97.87 % Rotamer: Outliers : 2.69 % Allowed : 13.46 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.27), residues: 890 helix: 1.01 (0.20), residues: 614 sheet: None (None), residues: 0 loop : 0.06 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 311 TYR 0.009 0.001 TYR D 162 PHE 0.011 0.001 PHE A 181 TRP 0.010 0.001 TRP F 184 HIS 0.001 0.000 HIS I 219 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7385) covalent geometry : angle 0.55760 ( 9980) hydrogen bonds : bond 0.04407 ( 435) hydrogen bonds : angle 4.76456 ( 1299) *********************** 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 245 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.408 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: 0.7264 (mm-30) cc_final: 0.6963 (mm-30) REVERT: A 216 ASP cc_start: 0.8753 (m-30) cc_final: 0.8427 (m-30) REVERT: A 286 PRO cc_start: 0.8470 (Cg_exo) cc_final: 0.8155 (Cg_endo) REVERT: D 253 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8148 (mptt) REVERT: D 272 LEU cc_start: 0.9082 (tt) cc_final: 0.8761 (tp) REVERT: D 291 ASP cc_start: 0.8156 (m-30) cc_final: 0.7943 (m-30) REVERT: D 292 GLN cc_start: 0.8951 (mt0) cc_final: 0.8485 (mp10) REVERT: F 164 LYS cc_start: 0.8658 (tptt) cc_final: 0.8271 (ttpp) REVERT: F 253 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8190 (tppt) REVERT: F 292 GLN cc_start: 0.8615 (mt0) cc_final: 0.8288 (tp-100) REVERT: I 164 LYS cc_start: 0.9081 (mttp) cc_final: 0.8879 (mtpt) REVERT: I 208 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8582 (mm-30) REVERT: I 218 MET cc_start: 0.9155 (tpp) cc_final: 0.8790 (tpt) REVERT: I 235 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8775 (mm-30) REVERT: I 238 LYS cc_start: 0.8892 (mttt) cc_final: 0.8500 (mtpp) REVERT: I 253 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7695 (tppt) REVERT: I 311 ARG cc_start: 0.9152 (mtp85) cc_final: 0.8261 (ttm110) REVERT: J 185 LEU cc_start: 0.9234 (tt) cc_final: 0.8991 (tt) REVERT: J 186 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8584 (tp30) REVERT: J 218 MET cc_start: 0.9232 (tpp) cc_final: 0.8753 (tpt) REVERT: J 254 TYR cc_start: 0.8851 (t80) cc_final: 0.8108 (t80) REVERT: J 283 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8217 (ttp-110) REVERT: J 296 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7578 (tm-30) REVERT: J 315 LEU cc_start: 0.7369 (mt) cc_final: 0.6927 (tp) outliers start: 21 outliers final: 14 residues processed: 231 average time/residue: 0.2506 time to fit residues: 72.9585 Evaluate side-chains 222 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 234 LEU 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 43 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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** I 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.112314 restraints weight = 38145.970| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 4.22 r_work: 0.3400 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.6176 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= 0.153 Angle : 0.553 6.137 9980 Z= 0.292 Chirality : 0.036 0.142 1105 Planarity : 0.005 0.104 1295 Dihedral : 4.771 21.420 987 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.36 % Favored : 97.42 % Rotamer: Outliers : 2.95 % Allowed : 14.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.27), residues: 890 helix: 1.16 (0.20), residues: 610 sheet: None (None), residues: 0 loop : 0.04 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.009 0.001 TYR D 162 PHE 0.013 0.001 PHE A 181 TRP 0.010 0.001 TRP D 184 HIS 0.001 0.000 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7385) covalent geometry : angle 0.55319 ( 9980) hydrogen bonds : bond 0.04307 ( 435) hydrogen bonds : angle 4.74436 ( 1299) *********************** 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 241 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.408 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: A 201 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7026 (mm-30) REVERT: A 216 ASP cc_start: 0.8782 (m-30) cc_final: 0.8448 (m-30) REVERT: A 222 GLN cc_start: 0.8581 (mt0) cc_final: 0.8329 (mt0) REVERT: A 232 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 286 PRO cc_start: 0.8465 (Cg_exo) cc_final: 0.8211 (Cg_endo) REVERT: A 328 MET cc_start: 0.8248 (tpt) cc_final: 0.7784 (tpt) REVERT: D 253 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8157 (mptt) REVERT: D 272 LEU cc_start: 0.9076 (tt) cc_final: 0.8752 (tp) REVERT: D 291 ASP cc_start: 0.8174 (m-30) cc_final: 0.7840 (m-30) REVERT: D 292 GLN cc_start: 0.8955 (mt0) cc_final: 0.8362 (mm-40) REVERT: D 326 GLN cc_start: 0.8803 (mt0) cc_final: 0.8559 (mt0) REVERT: F 194 GLU cc_start: 0.8418 (mp0) cc_final: 0.8149 (mp0) REVERT: F 253 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8208 (tppt) REVERT: F 283 ARG cc_start: 0.8546 (mtm110) cc_final: 0.8322 (ttm-80) REVERT: F 292 GLN cc_start: 0.8664 (mt0) cc_final: 0.8329 (tp-100) REVERT: I 164 LYS cc_start: 0.9031 (mttp) cc_final: 0.8804 (mtpt) REVERT: I 218 MET cc_start: 0.9137 (tpp) cc_final: 0.8806 (tpt) REVERT: I 235 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8762 (mm-30) REVERT: I 238 LYS cc_start: 0.8907 (mttt) cc_final: 0.8528 (mtpp) REVERT: I 253 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7766 (tppt) REVERT: I 296 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8761 (mm-30) REVERT: I 311 ARG cc_start: 0.9138 (mtp85) cc_final: 0.8216 (ttm110) REVERT: J 179 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8021 (mm-30) REVERT: J 185 LEU cc_start: 0.9255 (tt) cc_final: 0.8991 (tt) REVERT: J 218 MET cc_start: 0.9232 (tpp) cc_final: 0.8816 (tpt) REVERT: J 283 ARG cc_start: 0.8524 (mtp85) cc_final: 0.8169 (ttp-110) REVERT: J 296 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7521 (tm-30) REVERT: J 315 LEU cc_start: 0.7364 (mt) cc_final: 0.6945 (tp) outliers start: 23 outliers final: 18 residues processed: 228 average time/residue: 0.2646 time to fit residues: 76.1651 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 : 0.459 ------------------------------------------------------------------------------- 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 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 308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.139644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112166 restraints weight = 37658.871| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 4.14 r_work: 0.3402 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7385 Z= 0.159 Angle : 0.562 8.304 9980 Z= 0.294 Chirality : 0.036 0.143 1105 Planarity : 0.005 0.073 1295 Dihedral : 4.635 21.327 987 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.02 % Favored : 97.75 % Rotamer: Outliers : 2.56 % Allowed : 15.90 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.28), residues: 890 helix: 1.18 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.18 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.009 0.001 TYR D 162 PHE 0.014 0.001 PHE A 181 TRP 0.010 0.001 TRP D 184 HIS 0.001 0.000 HIS I 219 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7385) covalent geometry : angle 0.56228 ( 9980) hydrogen bonds : bond 0.04162 ( 435) hydrogen bonds : angle 4.68581 ( 1299) *********************** 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 240 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.573 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: 0.7328 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 216 ASP cc_start: 0.8783 (m-30) cc_final: 0.8429 (m-30) REVERT: A 222 GLN cc_start: 0.8581 (mt0) cc_final: 0.8303 (mt0) REVERT: A 232 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 286 PRO cc_start: 0.8501 (Cg_exo) cc_final: 0.8247 (Cg_endo) REVERT: A 328 MET cc_start: 0.8274 (tpt) cc_final: 0.7821 (tpt) REVERT: D 247 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7885 (ttm110) REVERT: D 253 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8159 (mptt) REVERT: D 272 LEU cc_start: 0.9082 (tt) cc_final: 0.8757 (tp) REVERT: D 291 ASP cc_start: 0.8158 (m-30) cc_final: 0.7827 (m-30) REVERT: D 292 GLN cc_start: 0.8959 (mt0) cc_final: 0.8340 (mm-40) REVERT: F 164 LYS cc_start: 0.8663 (tptt) cc_final: 0.8266 (ttpp) REVERT: F 253 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8199 (tppt) REVERT: F 283 ARG cc_start: 0.8511 (mtm110) cc_final: 0.8307 (ttm-80) REVERT: F 292 GLN cc_start: 0.8625 (mt0) cc_final: 0.8313 (tp-100) REVERT: I 164 LYS cc_start: 0.9016 (mttp) cc_final: 0.8816 (mtpt) REVERT: I 235 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8760 (mm-30) REVERT: I 238 LYS cc_start: 0.8901 (mttt) cc_final: 0.8520 (mtpp) REVERT: I 253 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7801 (tppt) REVERT: I 311 ARG cc_start: 0.9153 (mtp85) cc_final: 0.8243 (ttm110) REVERT: J 185 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8981 (tt) REVERT: J 218 MET cc_start: 0.9218 (tpp) cc_final: 0.8829 (tpt) REVERT: J 283 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8174 (ttp-110) REVERT: J 296 GLU cc_start: 0.8623 (mt-10) cc_final: 0.7547 (tm-30) REVERT: J 315 LEU cc_start: 0.7379 (mt) cc_final: 0.6986 (tp) outliers start: 20 outliers final: 18 residues processed: 228 average time/residue: 0.2596 time to fit residues: 75.1302 Evaluate side-chains 234 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 318 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.139166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111953 restraints weight = 37883.672| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 4.13 r_work: 0.3393 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6494 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= 0.165 Angle : 0.562 7.243 9980 Z= 0.294 Chirality : 0.036 0.144 1105 Planarity : 0.005 0.061 1295 Dihedral : 4.567 21.466 987 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.70 % Favored : 97.08 % Rotamer: Outliers : 2.69 % Allowed : 16.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.28), residues: 890 helix: 1.21 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.19 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.009 0.001 TYR D 162 PHE 0.014 0.001 PHE A 181 TRP 0.009 0.002 TRP D 309 HIS 0.001 0.000 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7385) covalent geometry : angle 0.56201 ( 9980) hydrogen bonds : bond 0.04140 ( 435) hydrogen bonds : angle 4.67160 ( 1299) *********************** 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 237 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.400 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: 0.7303 (mm-30) cc_final: 0.7011 (mm-30) REVERT: A 216 ASP cc_start: 0.8799 (m-30) cc_final: 0.8445 (m-30) REVERT: A 222 GLN cc_start: 0.8567 (mt0) cc_final: 0.8339 (mt0) REVERT: A 232 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 286 PRO cc_start: 0.8536 (Cg_exo) cc_final: 0.8288 (Cg_endo) REVERT: A 328 MET cc_start: 0.8254 (tpt) cc_final: 0.7803 (tpt) REVERT: D 177 GLU cc_start: 0.8542 (pt0) cc_final: 0.7630 (pp20) REVERT: D 239 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: D 247 ARG cc_start: 0.8147 (ttm110) cc_final: 0.7906 (ttm110) REVERT: D 253 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8154 (mptt) REVERT: D 272 LEU cc_start: 0.9083 (tt) cc_final: 0.8870 (tp) REVERT: D 291 ASP cc_start: 0.8174 (m-30) cc_final: 0.7829 (m-30) REVERT: D 292 GLN cc_start: 0.8917 (mt0) cc_final: 0.8290 (mm-40) REVERT: F 164 LYS cc_start: 0.8678 (tptt) cc_final: 0.8285 (ttpp) REVERT: F 194 GLU cc_start: 0.8530 (mp0) cc_final: 0.8220 (mp0) REVERT: F 253 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8201 (tppt) REVERT: F 292 GLN cc_start: 0.8626 (mt0) cc_final: 0.8305 (tp-100) REVERT: F 328 MET cc_start: 0.6138 (tpt) cc_final: 0.5668 (tpt) REVERT: I 164 LYS cc_start: 0.8990 (mttp) cc_final: 0.8774 (mtpt) REVERT: I 194 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8546 (mp0) REVERT: I 235 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8791 (mm-30) REVERT: I 238 LYS cc_start: 0.8912 (mttt) cc_final: 0.8541 (mtpp) REVERT: I 249 THR cc_start: 0.8147 (m) cc_final: 0.7875 (p) REVERT: I 253 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7810 (tppt) REVERT: I 296 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8787 (mm-30) REVERT: J 185 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8987 (tt) REVERT: J 218 MET cc_start: 0.9197 (tpp) cc_final: 0.8806 (tpt) REVERT: J 283 ARG cc_start: 0.8526 (mtp85) cc_final: 0.8189 (ttp-110) REVERT: J 296 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7565 (tm-30) REVERT: J 315 LEU cc_start: 0.7395 (mt) cc_final: 0.6998 (tp) outliers start: 21 outliers final: 18 residues processed: 225 average time/residue: 0.2524 time to fit residues: 71.8947 Evaluate side-chains 228 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain I residue 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 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 86 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.141273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.113594 restraints weight = 37847.040| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 4.22 r_work: 0.3412 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6584 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= 0.122 Angle : 0.539 7.163 9980 Z= 0.278 Chirality : 0.036 0.143 1105 Planarity : 0.005 0.054 1295 Dihedral : 4.417 20.939 987 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.36 % Favored : 97.42 % Rotamer: Outliers : 2.56 % Allowed : 16.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.28), residues: 890 helix: 1.38 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.22 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 166 TYR 0.009 0.001 TYR D 162 PHE 0.009 0.001 PHE A 181 TRP 0.009 0.001 TRP A 184 HIS 0.001 0.000 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7385) covalent geometry : angle 0.53945 ( 9980) hydrogen bonds : bond 0.03787 ( 435) hydrogen bonds : angle 4.48783 ( 1299) *********************** 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 237 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.403 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: 0.7340 (mm-30) cc_final: 0.7047 (mm-30) REVERT: A 216 ASP cc_start: 0.8801 (m-30) cc_final: 0.8449 (m-30) REVERT: A 232 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 286 PRO cc_start: 0.8509 (Cg_exo) cc_final: 0.8253 (Cg_endo) REVERT: A 328 MET cc_start: 0.8181 (tpt) cc_final: 0.7805 (tpt) REVERT: D 177 GLU cc_start: 0.8548 (pt0) cc_final: 0.7645 (pp20) REVERT: D 239 GLN cc_start: 0.8475 (mt0) cc_final: 0.7955 (mp10) REVERT: D 247 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7915 (ttm110) REVERT: D 253 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8133 (mptt) REVERT: D 291 ASP cc_start: 0.8159 (m-30) cc_final: 0.7828 (m-30) REVERT: D 292 GLN cc_start: 0.8880 (mt0) cc_final: 0.8219 (mm-40) REVERT: F 164 LYS cc_start: 0.8615 (tptt) cc_final: 0.8265 (ttpp) REVERT: F 194 GLU cc_start: 0.8543 (mp0) cc_final: 0.8220 (mp0) REVERT: F 253 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8180 (tppt) REVERT: F 256 ARG cc_start: 0.7616 (mmt-90) cc_final: 0.7277 (mmt-90) REVERT: F 292 GLN cc_start: 0.8620 (mt0) cc_final: 0.8290 (tp-100) REVERT: F 306 ASN cc_start: 0.6278 (m-40) cc_final: 0.5700 (t0) REVERT: F 328 MET cc_start: 0.5981 (tpt) cc_final: 0.5712 (tpt) REVERT: I 164 LYS cc_start: 0.8992 (mttp) cc_final: 0.8781 (mtpt) REVERT: I 194 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8612 (mp0) REVERT: I 235 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8809 (mm-30) REVERT: I 238 LYS cc_start: 0.8866 (mttt) cc_final: 0.8545 (mtpp) REVERT: I 249 THR cc_start: 0.8100 (m) cc_final: 0.7842 (p) REVERT: I 253 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7784 (tppt) REVERT: I 254 TYR cc_start: 0.8470 (t80) cc_final: 0.7218 (t80) REVERT: I 296 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8811 (mm-30) REVERT: J 185 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8952 (tt) REVERT: J 218 MET cc_start: 0.9208 (tpp) cc_final: 0.8827 (tpt) REVERT: J 283 ARG cc_start: 0.8519 (mtp85) cc_final: 0.8176 (ttp-110) REVERT: J 296 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7547 (tm-30) REVERT: J 315 LEU cc_start: 0.7379 (mt) cc_final: 0.7033 (tp) outliers start: 20 outliers final: 14 residues processed: 227 average time/residue: 0.2414 time to fit residues: 69.5747 Evaluate side-chains 223 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.111326 restraints weight = 38205.362| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 4.18 r_work: 0.3383 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.6690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7385 Z= 0.181 Angle : 0.570 6.657 9980 Z= 0.301 Chirality : 0.036 0.142 1105 Planarity : 0.005 0.056 1295 Dihedral : 4.453 21.751 987 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.40 % Rotamer: Outliers : 2.44 % Allowed : 16.92 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.28), residues: 890 helix: 1.25 (0.21), residues: 614 sheet: None (None), residues: 0 loop : 0.23 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 283 TYR 0.007 0.001 TYR D 162 PHE 0.016 0.001 PHE A 181 TRP 0.009 0.001 TRP I 184 HIS 0.001 0.000 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7385) covalent geometry : angle 0.57048 ( 9980) hydrogen bonds : bond 0.04099 ( 435) hydrogen bonds : angle 4.66009 ( 1299) *********************** 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 229 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7052 (mm-30) REVERT: A 216 ASP cc_start: 0.8821 (m-30) cc_final: 0.8471 (m-30) REVERT: A 232 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 286 PRO cc_start: 0.8551 (Cg_exo) cc_final: 0.8303 (Cg_endo) REVERT: A 328 MET cc_start: 0.8213 (tpt) cc_final: 0.7766 (tpt) REVERT: D 177 GLU cc_start: 0.8587 (pt0) cc_final: 0.7741 (pp20) REVERT: D 225 ASN cc_start: 0.7647 (t0) cc_final: 0.7391 (t0) REVERT: D 239 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7984 (mp10) REVERT: D 247 ARG cc_start: 0.8245 (ttm110) cc_final: 0.8026 (ttm110) REVERT: D 253 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8422 (tptt) REVERT: D 272 LEU cc_start: 0.9089 (tt) cc_final: 0.8764 (tp) REVERT: D 291 ASP cc_start: 0.8157 (m-30) cc_final: 0.7824 (m-30) REVERT: D 292 GLN cc_start: 0.8897 (mt0) cc_final: 0.8218 (mm-40) REVERT: D 326 GLN cc_start: 0.8692 (mt0) cc_final: 0.8453 (mt0) REVERT: F 164 LYS cc_start: 0.8754 (tptt) cc_final: 0.8418 (ttpp) REVERT: F 194 GLU cc_start: 0.8594 (mp0) cc_final: 0.8268 (mp0) REVERT: F 253 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8203 (tppt) REVERT: F 256 ARG cc_start: 0.7619 (mmt-90) cc_final: 0.7280 (mmt-90) REVERT: F 292 GLN cc_start: 0.8642 (mt0) cc_final: 0.8317 (tp-100) REVERT: F 306 ASN cc_start: 0.6306 (m-40) cc_final: 0.5712 (t0) REVERT: F 328 MET cc_start: 0.5968 (tpt) cc_final: 0.5713 (tpt) REVERT: I 194 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8582 (mp0) REVERT: I 235 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8778 (mm-30) REVERT: I 238 LYS cc_start: 0.8895 (mttt) cc_final: 0.8562 (mtpp) REVERT: I 249 THR cc_start: 0.8131 (m) cc_final: 0.7870 (p) REVERT: I 253 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7834 (tppt) REVERT: J 185 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8997 (tt) REVERT: J 218 MET cc_start: 0.9197 (tpp) cc_final: 0.8839 (tpt) REVERT: J 283 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8180 (ttp-110) REVERT: J 296 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7559 (tm-30) REVERT: J 315 LEU cc_start: 0.7387 (mt) cc_final: 0.7007 (tp) outliers start: 19 outliers final: 14 residues processed: 218 average time/residue: 0.2500 time to fit residues: 69.3876 Evaluate side-chains 221 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 239 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3835 r_free = 0.3835 target = 0.137340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.110349 restraints weight = 38136.116| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 4.10 r_work: 0.3358 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7385 Z= 0.232 Angle : 0.600 6.444 9980 Z= 0.320 Chirality : 0.037 0.145 1105 Planarity : 0.005 0.043 1295 Dihedral : 4.599 23.558 987 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.15 % Favored : 96.63 % Rotamer: Outliers : 2.18 % Allowed : 17.18 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.28), residues: 890 helix: 1.12 (0.21), residues: 614 sheet: None (None), residues: 0 loop : 0.14 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 166 TYR 0.008 0.001 TYR D 268 PHE 0.017 0.002 PHE A 181 TRP 0.010 0.002 TRP I 184 HIS 0.001 0.000 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 7385) covalent geometry : angle 0.60039 ( 9980) hydrogen bonds : bond 0.04425 ( 435) hydrogen bonds : angle 4.84278 ( 1299) ********************** 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 234 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.353 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: 0.7372 (mm-30) cc_final: 0.7087 (mm-30) REVERT: A 216 ASP cc_start: 0.8858 (m-30) cc_final: 0.8508 (m-30) REVERT: A 222 GLN cc_start: 0.8546 (mt0) cc_final: 0.8339 (mt0) REVERT: A 232 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 286 PRO cc_start: 0.8576 (Cg_exo) cc_final: 0.8351 (Cg_endo) REVERT: A 328 MET cc_start: 0.8265 (tpt) cc_final: 0.7761 (tpt) REVERT: D 177 GLU cc_start: 0.8577 (pt0) cc_final: 0.7744 (pp20) REVERT: D 225 ASN cc_start: 0.7693 (t0) cc_final: 0.7433 (t0) REVERT: D 239 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: D 247 ARG cc_start: 0.8247 (ttm110) cc_final: 0.8043 (ttm110) REVERT: D 253 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8450 (tptt) REVERT: D 268 TYR cc_start: 0.8268 (t80) cc_final: 0.7624 (t80) REVERT: D 272 LEU cc_start: 0.9090 (tt) cc_final: 0.8824 (tp) REVERT: D 291 ASP cc_start: 0.8206 (m-30) cc_final: 0.7937 (m-30) REVERT: D 292 GLN cc_start: 0.8965 (mt0) cc_final: 0.8326 (mm-40) REVERT: D 326 GLN cc_start: 0.8739 (mt0) cc_final: 0.8527 (mt0) REVERT: F 164 LYS cc_start: 0.8799 (tptt) cc_final: 0.8425 (ttpp) REVERT: F 253 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8215 (tppt) REVERT: F 292 GLN cc_start: 0.8631 (mt0) cc_final: 0.8314 (tp-100) REVERT: F 306 ASN cc_start: 0.6344 (m-40) cc_final: 0.5721 (t0) REVERT: F 328 MET cc_start: 0.6017 (tpt) cc_final: 0.5764 (tpt) REVERT: I 194 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8575 (mp0) REVERT: I 235 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8785 (mm-30) REVERT: I 238 LYS cc_start: 0.8932 (mttt) cc_final: 0.8585 (mtpp) REVERT: I 249 THR cc_start: 0.8118 (m) cc_final: 0.7858 (p) REVERT: I 253 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7890 (tppt) REVERT: J 185 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9022 (tt) REVERT: J 218 MET cc_start: 0.9193 (tpp) cc_final: 0.8893 (tpt) REVERT: J 283 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8198 (ttp-110) REVERT: J 315 LEU cc_start: 0.7357 (mt) cc_final: 0.6976 (tp) outliers start: 17 outliers final: 15 residues processed: 224 average time/residue: 0.2707 time to fit residues: 75.8977 Evaluate side-chains 229 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 239 GLN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 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 46 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.141849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114336 restraints weight = 37603.527| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 4.17 r_work: 0.3420 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.6871 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= 0.112 Angle : 0.554 6.857 9980 Z= 0.284 Chirality : 0.036 0.141 1105 Planarity : 0.005 0.055 1295 Dihedral : 4.357 21.313 987 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.47 % Favored : 97.30 % Rotamer: Outliers : 1.67 % Allowed : 17.82 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.28), residues: 890 helix: 1.41 (0.21), residues: 614 sheet: None (None), residues: 0 loop : 0.23 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 283 TYR 0.012 0.001 TYR D 162 PHE 0.007 0.001 PHE F 181 TRP 0.012 0.001 TRP F 205 HIS 0.002 0.000 HIS F 219 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7385) covalent geometry : angle 0.55430 ( 9980) hydrogen bonds : bond 0.03646 ( 435) hydrogen bonds : angle 4.40348 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3828.57 seconds wall clock time: 65 minutes 34.27 seconds (3934.27 seconds total)