Starting phenix.real_space_refine on Tue May 7 06:09:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrz_37795/05_2024/8wrz_37795_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrz_37795/05_2024/8wrz_37795.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrz_37795/05_2024/8wrz_37795_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrz_37795/05_2024/8wrz_37795_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrz_37795/05_2024/8wrz_37795_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrz_37795/05_2024/8wrz_37795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrz_37795/05_2024/8wrz_37795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrz_37795/05_2024/8wrz_37795_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrz_37795/05_2024/8wrz_37795_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 85 atoms to isotropic. 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 P 5 5.49 5 S 37 5.16 5 C 4455 2.51 5 N 1160 2.21 5 O 1257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 6914 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2783 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 25, 'TRANS': 326} Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 920 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "R" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2266 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Chain breaks: 1 Chain: "V" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 91 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'8D0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.06, per 1000 atoms: 0.59 Number of scatterers: 6914 At special positions: 0 Unit cell: (80.08, 102.96, 145.6, 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 37 16.00 P 5 15.00 O 1257 8.00 N 1160 7.00 C 4455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 9 sheets defined 29.3% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 67 through 70 No H-bonds generated for 'chain 'A' and resid 67 through 70' Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 157 through 162 removed outlier: 4.253A pdb=" N ARG A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 162' Processing helix chain 'A' and resid 280 through 283 removed outlier: 4.343A pdb=" N GLU A 283 " --> pdb=" O ASN A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'R' and resid 115 through 143 removed outlier: 3.953A pdb=" N LEU R 122 " --> pdb=" O ALA R 118 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER R 123 " --> pdb=" O ILE R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 148 Processing helix chain 'R' and resid 151 through 177 removed outlier: 3.612A pdb=" N GLY R 166 " --> pdb=" O ALA R 162 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL R 168 " --> pdb=" O LEU R 164 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 219 removed outlier: 4.315A pdb=" N LYS R 192 " --> pdb=" O VAL R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 227 removed outlier: 4.225A pdb=" N LYS R 225 " --> pdb=" O PRO R 221 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 253 Proline residue: R 251 - end of helix Processing helix chain 'R' and resid 273 through 311 removed outlier: 3.780A pdb=" N ILE R 280 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG R 307 " --> pdb=" O SER R 303 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 366 removed outlier: 4.083A pdb=" N THR R 344 " --> pdb=" O GLU R 340 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) Proline residue: R 358 - end of helix removed outlier: 3.643A pdb=" N TYR R 365 " --> pdb=" O ALA R 361 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP R 366 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 373 through 398 removed outlier: 3.950A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS R 386 " --> pdb=" O CYS R 382 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU R 387 " --> pdb=" O SER R 383 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 402 through 410 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.586A pdb=" N LEU A 22 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.607A pdb=" N ARG A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 81 through 85 removed outlier: 3.754A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 183 through 188 Processing sheet with id= E, first strand: chain 'A' and resid 343 through 349 removed outlier: 3.620A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 238 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 322 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 254 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= G, first strand: chain 'H' and resid 96 through 103 removed outlier: 5.586A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= I, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.157A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 861 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: 1.82 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1068 1.29 - 1.42: 1848 1.42 - 1.55: 4084 1.55 - 1.68: 19 1.68 - 1.81: 51 Bond restraints: 7070 Sorted by residual: bond pdb=" C26 8D0 R 501 " pdb=" N1 8D0 R 501 " ideal model delta sigma weight residual 1.512 1.158 0.354 2.00e-02 2.50e+03 3.13e+02 bond pdb=" C6 8D0 R 501 " pdb=" O1 8D0 R 501 " ideal model delta sigma weight residual 1.594 1.369 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C26 8D0 R 501 " pdb=" S1 8D0 R 501 " ideal model delta sigma weight residual 1.787 1.587 0.200 2.00e-02 2.50e+03 9.98e+01 bond pdb=" C10 8D0 R 501 " pdb=" C11 8D0 R 501 " ideal model delta sigma weight residual 1.338 1.523 -0.185 2.00e-02 2.50e+03 8.52e+01 bond pdb=" C23 8D0 R 501 " pdb=" C24 8D0 R 501 " ideal model delta sigma weight residual 1.346 1.521 -0.175 2.00e-02 2.50e+03 7.64e+01 ... (remaining 7065 not shown) Histogram of bond angle deviations from ideal: 99.42 - 114.76: 4477 114.76 - 130.10: 5087 130.10 - 145.44: 37 145.44 - 160.78: 1 160.78 - 176.12: 1 Bond angle restraints: 9603 Sorted by residual: angle pdb=" C25 8D0 R 501 " pdb=" N1 8D0 R 501 " pdb=" C26 8D0 R 501 " ideal model delta sigma weight residual 119.40 156.12 -36.72 3.00e+00 1.11e-01 1.50e+02 angle pdb=" CB TPO V 359 " pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 119.31 106.50 12.81 3.00e+00 1.11e-01 1.82e+01 angle pdb=" CB TPO V 360 " pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 119.31 106.63 12.68 3.00e+00 1.11e-01 1.79e+01 angle pdb=" CB MET R 308 " pdb=" CG MET R 308 " pdb=" SD MET R 308 " ideal model delta sigma weight residual 112.70 124.23 -11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C CYS A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 122.10 116.05 6.05 1.66e+00 3.63e-01 1.33e+01 ... (remaining 9598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 3899 18.18 - 36.36: 278 36.36 - 54.53: 46 54.53 - 72.71: 11 72.71 - 90.89: 3 Dihedral angle restraints: 4237 sinusoidal: 1678 harmonic: 2559 Sorted by residual: dihedral pdb=" CA PHE R 268 " pdb=" C PHE R 268 " pdb=" N PRO R 269 " pdb=" CA PRO R 269 " ideal model delta harmonic sigma weight residual -180.00 -154.79 -25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA PHE A 149 " pdb=" C PHE A 149 " pdb=" N CYS A 150 " pdb=" CA CYS A 150 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 129.37 -36.37 1 1.00e+01 1.00e-02 1.87e+01 ... (remaining 4234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 966 0.074 - 0.148: 135 0.148 - 0.222: 4 0.222 - 0.296: 0 0.296 - 0.370: 1 Chirality restraints: 1106 Sorted by residual: chirality pdb=" C11 8D0 R 501 " pdb=" C10 8D0 R 501 " pdb=" C12 8D0 R 501 " pdb=" C14 8D0 R 501 " both_signs ideal model delta sigma weight residual False -2.87 -2.50 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA LYS A 292 " pdb=" N LYS A 292 " pdb=" C LYS A 292 " pdb=" CB LYS A 292 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU R 207 " pdb=" CB LEU R 207 " pdb=" CD1 LEU R 207 " pdb=" CD2 LEU R 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.29e-01 ... (remaining 1103 not shown) Planarity restraints: 1187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 241 " 0.027 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP R 241 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP R 241 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP R 241 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 241 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 241 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 241 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 241 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 241 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 241 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 88 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO A 89 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 43 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO H 44 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 44 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 44 " -0.034 5.00e-02 4.00e+02 ... (remaining 1184 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 550 2.73 - 3.28: 7194 3.28 - 3.82: 11265 3.82 - 4.36: 12771 4.36 - 4.90: 21760 Nonbonded interactions: 53540 Sorted by model distance: nonbonded pdb=" OD1 ASN R 256 " pdb=" O HIS R 270 " model vdw 2.192 3.040 nonbonded pdb=" O VAL R 196 " pdb=" OG SER R 199 " model vdw 2.199 2.440 nonbonded pdb=" O VAL H 32 " pdb=" OG SER H 56 " model vdw 2.236 2.440 nonbonded pdb=" OD1 ASN A 222 " pdb=" O LYS A 226 " model vdw 2.242 3.040 nonbonded pdb=" OG SER H 36 " pdb=" OG SER H 102 " model vdw 2.254 2.440 ... (remaining 53535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 3.690 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.510 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 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 : 0.010 0.354 7070 Z= 0.602 Angle : 0.955 36.718 9603 Z= 0.455 Chirality : 0.049 0.370 1106 Planarity : 0.006 0.075 1187 Dihedral : 12.847 90.890 2581 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.13 % Allowed : 0.53 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.28), residues: 854 helix: 0.44 (0.32), residues: 244 sheet: 0.47 (0.34), residues: 235 loop : -1.50 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP R 241 HIS 0.008 0.001 HIS A 219 PHE 0.021 0.002 PHE R 170 TYR 0.018 0.002 TYR R 224 ARG 0.008 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 281 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8463 (t) cc_final: 0.8247 (m) REVERT: A 61 PHE cc_start: 0.7051 (t80) cc_final: 0.6653 (t80) REVERT: A 106 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8517 (ttmt) REVERT: A 147 LYS cc_start: 0.7612 (ttpt) cc_final: 0.7046 (ttpt) REVERT: A 176 GLU cc_start: 0.7246 (pm20) cc_final: 0.6275 (pm20) REVERT: A 185 GLU cc_start: 0.7462 (pt0) cc_final: 0.7140 (pt0) REVERT: A 212 GLU cc_start: 0.7965 (tt0) cc_final: 0.7680 (tt0) REVERT: A 217 ASN cc_start: 0.7783 (m-40) cc_final: 0.7566 (m-40) REVERT: A 233 ILE cc_start: 0.8315 (mp) cc_final: 0.7992 (mp) REVERT: A 248 GLN cc_start: 0.7336 (pt0) cc_final: 0.6830 (pt0) REVERT: A 257 GLU cc_start: 0.6755 (mp0) cc_final: 0.6113 (mp0) REVERT: A 273 THR cc_start: 0.8835 (t) cc_final: 0.8485 (p) REVERT: H 49 GLU cc_start: 0.7532 (tt0) cc_final: 0.7177 (tt0) REVERT: H 57 TYR cc_start: 0.8934 (t80) cc_final: 0.8548 (t80) REVERT: H 76 ASP cc_start: 0.8790 (t0) cc_final: 0.8123 (t0) REVERT: H 80 ASN cc_start: 0.9089 (t0) cc_final: 0.8745 (t0) REVERT: H 81 THR cc_start: 0.8562 (p) cc_final: 0.8032 (p) REVERT: H 83 TYR cc_start: 0.7369 (m-80) cc_final: 0.7050 (m-80) REVERT: L 4 GLN cc_start: 0.7526 (tt0) cc_final: 0.7257 (tt0) REVERT: L 5 MET cc_start: 0.7237 (ttt) cc_final: 0.6507 (ttt) REVERT: L 43 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8750 (mmpt) REVERT: L 46 LYS cc_start: 0.8292 (pttm) cc_final: 0.7473 (pttm) REVERT: L 56 TYR cc_start: 0.7743 (t80) cc_final: 0.7526 (t80) REVERT: L 74 LEU cc_start: 0.6767 (tt) cc_final: 0.5646 (tt) REVERT: L 83 ASP cc_start: 0.8007 (m-30) cc_final: 0.7382 (m-30) REVERT: L 89 CYS cc_start: 0.7385 (p) cc_final: 0.6951 (p) REVERT: L 90 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7723 (pp30) REVERT: R 209 LEU cc_start: 0.7523 (tp) cc_final: 0.7304 (tp) REVERT: R 214 ARG cc_start: 0.8364 (mtt180) cc_final: 0.8131 (mtt180) REVERT: R 337 MET cc_start: 0.4418 (ttp) cc_final: 0.4145 (ttp) REVERT: R 360 LEU cc_start: 0.8299 (mt) cc_final: 0.8035 (mt) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.2204 time to fit residues: 78.9583 Evaluate side-chains 262 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.0870 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 223 ASN H 104 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7070 Z= 0.210 Angle : 0.751 12.864 9603 Z= 0.364 Chirality : 0.046 0.406 1106 Planarity : 0.005 0.055 1187 Dihedral : 8.044 88.868 985 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.11 % Allowed : 15.57 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.28), residues: 854 helix: 0.51 (0.32), residues: 247 sheet: 0.56 (0.32), residues: 242 loop : -1.38 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 241 HIS 0.004 0.001 HIS H 38 PHE 0.034 0.002 PHE A 244 TYR 0.029 0.001 TYR R 365 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 265 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7296 (ttpt) REVERT: A 19 THR cc_start: 0.8572 (t) cc_final: 0.8319 (m) REVERT: A 61 PHE cc_start: 0.7017 (t80) cc_final: 0.6638 (t80) REVERT: A 106 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8483 (ttmt) REVERT: A 111 HIS cc_start: 0.7735 (m-70) cc_final: 0.7095 (m-70) REVERT: A 147 LYS cc_start: 0.7551 (ttpt) cc_final: 0.6719 (ttpt) REVERT: A 176 GLU cc_start: 0.6860 (pm20) cc_final: 0.6422 (pm20) REVERT: A 177 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7167 (ttp80) REVERT: A 185 GLU cc_start: 0.7541 (pt0) cc_final: 0.7233 (pt0) REVERT: A 212 GLU cc_start: 0.8041 (tt0) cc_final: 0.7773 (tt0) REVERT: A 217 ASN cc_start: 0.7791 (m-40) cc_final: 0.7585 (m-40) REVERT: A 233 ILE cc_start: 0.8419 (mp) cc_final: 0.8167 (mp) REVERT: A 236 ARG cc_start: 0.7515 (mtt-85) cc_final: 0.6943 (mtt-85) REVERT: A 248 GLN cc_start: 0.7312 (pt0) cc_final: 0.6879 (pt0) REVERT: A 256 GLU cc_start: 0.7237 (tp30) cc_final: 0.7017 (tp30) REVERT: A 281 ASN cc_start: 0.8372 (m-40) cc_final: 0.8124 (m110) REVERT: A 323 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7741 (p) REVERT: A 324 LYS cc_start: 0.7833 (ptpp) cc_final: 0.7023 (ptpp) REVERT: H 46 LYS cc_start: 0.7385 (mtmm) cc_final: 0.7036 (ptpp) REVERT: H 49 GLU cc_start: 0.7494 (tt0) cc_final: 0.7133 (tt0) REVERT: H 76 ASP cc_start: 0.8802 (t0) cc_final: 0.8120 (t0) REVERT: H 80 ASN cc_start: 0.9079 (t0) cc_final: 0.8832 (t0) REVERT: H 83 TYR cc_start: 0.7362 (m-80) cc_final: 0.6963 (m-80) REVERT: H 113 TRP cc_start: 0.7057 (t-100) cc_final: 0.6221 (t-100) REVERT: L 4 GLN cc_start: 0.7542 (tt0) cc_final: 0.7294 (tt0) REVERT: L 5 MET cc_start: 0.7314 (ttt) cc_final: 0.6421 (ttt) REVERT: L 19 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8467 (mmm-85) REVERT: L 38 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7990 (tm-30) REVERT: L 39 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7670 (tm-30) REVERT: L 46 LYS cc_start: 0.8104 (pttm) cc_final: 0.7787 (pttm) REVERT: L 62 ARG cc_start: 0.6818 (ptm-80) cc_final: 0.6523 (ptt180) REVERT: L 74 LEU cc_start: 0.6828 (tt) cc_final: 0.5844 (tt) REVERT: L 83 ASP cc_start: 0.7761 (m-30) cc_final: 0.7483 (m-30) REVERT: L 88 TYR cc_start: 0.7524 (m-80) cc_final: 0.7005 (m-10) REVERT: L 89 CYS cc_start: 0.7574 (p) cc_final: 0.6475 (p) REVERT: L 90 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7970 (pt0) REVERT: R 150 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.6836 (mtm-85) REVERT: R 207 LEU cc_start: 0.8733 (mt) cc_final: 0.8458 (mt) REVERT: R 214 ARG cc_start: 0.8475 (mtt180) cc_final: 0.8034 (mtt180) REVERT: R 241 TRP cc_start: 0.7065 (m-10) cc_final: 0.6779 (m-10) REVERT: R 337 MET cc_start: 0.4432 (ttp) cc_final: 0.4178 (ttp) REVERT: R 356 TRP cc_start: 0.7063 (m-90) cc_final: 0.6288 (m-90) REVERT: R 385 LEU cc_start: 0.8326 (mt) cc_final: 0.8039 (mt) outliers start: 16 outliers final: 9 residues processed: 268 average time/residue: 0.2225 time to fit residues: 75.6611 Evaluate side-chains 261 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 250 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain R residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7070 Z= 0.287 Angle : 0.754 12.219 9603 Z= 0.376 Chirality : 0.046 0.222 1106 Planarity : 0.005 0.060 1187 Dihedral : 7.993 87.073 985 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.88 % Allowed : 17.94 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.28), residues: 854 helix: 0.59 (0.32), residues: 249 sheet: 0.42 (0.32), residues: 243 loop : -1.37 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP L 36 HIS 0.008 0.001 HIS A 111 PHE 0.047 0.003 PHE A 244 TYR 0.029 0.002 TYR R 275 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7218 (ttpt) REVERT: A 49 LYS cc_start: 0.8400 (mmpt) cc_final: 0.8074 (mmpt) REVERT: A 61 PHE cc_start: 0.7056 (t80) cc_final: 0.6681 (t80) REVERT: A 80 PHE cc_start: 0.8321 (t80) cc_final: 0.8107 (t80) REVERT: A 83 ASN cc_start: 0.7127 (OUTLIER) cc_final: 0.6882 (m-40) REVERT: A 106 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8501 (ttmt) REVERT: A 147 LYS cc_start: 0.7142 (ttpt) cc_final: 0.6885 (ttpt) REVERT: A 156 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6585 (tm-30) REVERT: A 176 GLU cc_start: 0.6954 (pm20) cc_final: 0.6481 (pm20) REVERT: A 177 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7305 (ttp80) REVERT: A 185 GLU cc_start: 0.7628 (pt0) cc_final: 0.7331 (pt0) REVERT: A 212 GLU cc_start: 0.8056 (tt0) cc_final: 0.7822 (tt0) REVERT: A 233 ILE cc_start: 0.8351 (mp) cc_final: 0.8070 (mp) REVERT: A 236 ARG cc_start: 0.7653 (mtt-85) cc_final: 0.6801 (mtt-85) REVERT: A 237 GLN cc_start: 0.7547 (tt0) cc_final: 0.7268 (tt0) REVERT: A 248 GLN cc_start: 0.7419 (pt0) cc_final: 0.7067 (pt0) REVERT: A 255 MET cc_start: 0.7401 (tpt) cc_final: 0.6147 (tpt) REVERT: A 256 GLU cc_start: 0.7543 (tp30) cc_final: 0.7047 (tp30) REVERT: A 257 GLU cc_start: 0.7039 (mp0) cc_final: 0.6224 (mp0) REVERT: A 270 LYS cc_start: 0.7580 (ptmm) cc_final: 0.5833 (ttpp) REVERT: A 281 ASN cc_start: 0.8462 (m-40) cc_final: 0.8150 (m110) REVERT: A 320 SER cc_start: 0.8486 (t) cc_final: 0.7923 (p) REVERT: A 323 VAL cc_start: 0.7994 (OUTLIER) cc_final: 0.7791 (p) REVERT: A 324 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7133 (ptpp) REVERT: A 355 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7199 (mtmt) REVERT: H 49 GLU cc_start: 0.7541 (tt0) cc_final: 0.7206 (tt0) REVERT: H 57 TYR cc_start: 0.8930 (t80) cc_final: 0.8678 (t80) REVERT: H 76 ASP cc_start: 0.8762 (t0) cc_final: 0.8248 (t0) REVERT: H 80 ASN cc_start: 0.9117 (t0) cc_final: 0.8851 (t0) REVERT: H 83 TYR cc_start: 0.7414 (m-80) cc_final: 0.7030 (m-80) REVERT: L 5 MET cc_start: 0.7254 (ttt) cc_final: 0.6245 (ttt) REVERT: L 19 ARG cc_start: 0.8767 (tpp80) cc_final: 0.8450 (mmm-85) REVERT: L 28 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7266 (tm-30) REVERT: L 38 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8083 (tm-30) REVERT: L 39 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7782 (tm-30) REVERT: L 46 LYS cc_start: 0.8066 (pttm) cc_final: 0.7737 (pttm) REVERT: L 88 TYR cc_start: 0.7545 (m-80) cc_final: 0.7291 (m-10) REVERT: L 89 CYS cc_start: 0.7548 (p) cc_final: 0.6856 (p) REVERT: L 90 GLN cc_start: 0.8354 (pp30) cc_final: 0.7970 (pt0) REVERT: R 150 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7093 (mtm-85) REVERT: R 207 LEU cc_start: 0.8778 (mt) cc_final: 0.8415 (mt) REVERT: R 208 PHE cc_start: 0.8211 (t80) cc_final: 0.7795 (t80) REVERT: R 214 ARG cc_start: 0.8450 (mtt180) cc_final: 0.8022 (mtt180) REVERT: R 275 TYR cc_start: 0.4901 (OUTLIER) cc_final: 0.3329 (m-80) REVERT: R 337 MET cc_start: 0.4467 (ttp) cc_final: 0.4226 (ttp) REVERT: R 347 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7435 (tt) REVERT: R 352 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7976 (mm) REVERT: R 356 TRP cc_start: 0.7150 (m-90) cc_final: 0.6512 (m-90) REVERT: R 385 LEU cc_start: 0.8461 (mt) cc_final: 0.8167 (mt) outliers start: 37 outliers final: 21 residues processed: 283 average time/residue: 0.2170 time to fit residues: 77.6760 Evaluate side-chains 290 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 262 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7070 Z= 0.316 Angle : 0.760 12.347 9603 Z= 0.381 Chirality : 0.046 0.206 1106 Planarity : 0.005 0.055 1187 Dihedral : 7.917 86.685 982 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.54 % Allowed : 20.71 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.28), residues: 854 helix: 0.46 (0.31), residues: 254 sheet: 0.23 (0.33), residues: 240 loop : -1.51 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP L 36 HIS 0.005 0.001 HIS R 178 PHE 0.044 0.002 PHE A 244 TYR 0.026 0.002 TYR A 238 ARG 0.006 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 261 time to evaluate : 0.805 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: A 10 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7223 (ttpt) REVERT: A 61 PHE cc_start: 0.7066 (t80) cc_final: 0.6652 (t80) REVERT: A 77 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7733 (mmtm) REVERT: A 104 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8014 (tt) REVERT: A 106 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8534 (ttmt) REVERT: A 128 THR cc_start: 0.8264 (m) cc_final: 0.7942 (p) REVERT: A 145 GLU cc_start: 0.6500 (tm-30) cc_final: 0.5741 (tm-30) REVERT: A 147 LYS cc_start: 0.7202 (ttpt) cc_final: 0.6654 (ttpt) REVERT: A 156 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6542 (tm-30) REVERT: A 176 GLU cc_start: 0.7199 (pm20) cc_final: 0.6686 (pm20) REVERT: A 177 ARG cc_start: 0.7573 (ttp80) cc_final: 0.7342 (ttp80) REVERT: A 212 GLU cc_start: 0.8116 (tt0) cc_final: 0.7844 (tt0) REVERT: A 233 ILE cc_start: 0.8430 (mp) cc_final: 0.8158 (mp) REVERT: A 236 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7301 (mtt-85) REVERT: A 237 GLN cc_start: 0.7644 (tt0) cc_final: 0.7325 (tt0) REVERT: A 255 MET cc_start: 0.7436 (tpt) cc_final: 0.7174 (tpt) REVERT: A 256 GLU cc_start: 0.7525 (tp30) cc_final: 0.7086 (tp30) REVERT: A 257 GLU cc_start: 0.7300 (mp0) cc_final: 0.6336 (mp0) REVERT: A 270 LYS cc_start: 0.7701 (ptmm) cc_final: 0.6283 (ttpt) REVERT: A 281 ASN cc_start: 0.8465 (m-40) cc_final: 0.8043 (m-40) REVERT: A 320 SER cc_start: 0.8550 (t) cc_final: 0.7781 (p) REVERT: A 323 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 355 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7212 (mtmt) REVERT: H 25 CYS cc_start: 0.4889 (t) cc_final: 0.4401 (t) REVERT: H 49 GLU cc_start: 0.7596 (tt0) cc_final: 0.7268 (tt0) REVERT: H 57 TYR cc_start: 0.8844 (t80) cc_final: 0.8642 (t80) REVERT: H 76 ASP cc_start: 0.8743 (t0) cc_final: 0.8260 (t0) REVERT: H 80 ASN cc_start: 0.9151 (t0) cc_final: 0.8920 (t0) REVERT: H 83 TYR cc_start: 0.7408 (m-80) cc_final: 0.6964 (m-80) REVERT: L 5 MET cc_start: 0.7288 (ttt) cc_final: 0.6228 (ttt) REVERT: L 19 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8409 (mmm-85) REVERT: L 28 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7143 (tm-30) REVERT: L 38 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8126 (tm-30) REVERT: L 39 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7725 (tm-30) REVERT: L 46 LYS cc_start: 0.8074 (pttm) cc_final: 0.7680 (pttm) REVERT: L 88 TYR cc_start: 0.7529 (m-80) cc_final: 0.7251 (m-10) REVERT: L 89 CYS cc_start: 0.7412 (p) cc_final: 0.6657 (p) REVERT: L 90 GLN cc_start: 0.8283 (pp30) cc_final: 0.7403 (pp30) REVERT: L 106 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.7989 (pp20) REVERT: R 150 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7113 (mtm-85) REVERT: R 207 LEU cc_start: 0.8795 (mt) cc_final: 0.8443 (mt) REVERT: R 208 PHE cc_start: 0.8183 (t80) cc_final: 0.7742 (t80) REVERT: R 214 ARG cc_start: 0.8427 (mtt180) cc_final: 0.8023 (mtt180) REVERT: R 337 MET cc_start: 0.4455 (ttp) cc_final: 0.4200 (ttp) REVERT: R 352 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7888 (mm) REVERT: R 356 TRP cc_start: 0.7130 (m-90) cc_final: 0.6419 (m-90) REVERT: R 385 LEU cc_start: 0.8476 (mt) cc_final: 0.8181 (mt) outliers start: 42 outliers final: 27 residues processed: 282 average time/residue: 0.2129 time to fit residues: 76.7710 Evaluate side-chains 291 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 259 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 396 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 0.0060 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.0040 chunk 73 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7070 Z= 0.169 Angle : 0.704 12.258 9603 Z= 0.340 Chirality : 0.044 0.190 1106 Planarity : 0.004 0.050 1187 Dihedral : 7.534 85.002 982 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.49 % Allowed : 24.27 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.29), residues: 854 helix: 0.87 (0.33), residues: 250 sheet: 0.36 (0.33), residues: 234 loop : -1.28 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP L 36 HIS 0.004 0.001 HIS A 159 PHE 0.049 0.002 PHE A 244 TYR 0.028 0.001 TYR A 238 ARG 0.003 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 254 time to evaluate : 0.761 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: A 10 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7203 (ttpt) REVERT: A 17 LYS cc_start: 0.7536 (tttt) cc_final: 0.7028 (tttp) REVERT: A 59 CYS cc_start: 0.7782 (t) cc_final: 0.7507 (p) REVERT: A 61 PHE cc_start: 0.6976 (t80) cc_final: 0.6654 (t80) REVERT: A 80 PHE cc_start: 0.8300 (t80) cc_final: 0.8097 (t80) REVERT: A 104 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7903 (tt) REVERT: A 106 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8506 (ttmt) REVERT: A 145 GLU cc_start: 0.6356 (tm-30) cc_final: 0.5559 (tm-30) REVERT: A 147 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6633 (ttpt) REVERT: A 156 GLU cc_start: 0.6647 (tm-30) cc_final: 0.6269 (tm-30) REVERT: A 169 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6601 (pmt-80) REVERT: A 176 GLU cc_start: 0.7087 (pm20) cc_final: 0.6838 (pm20) REVERT: A 177 ARG cc_start: 0.7435 (ttp80) cc_final: 0.7203 (ttp80) REVERT: A 185 GLU cc_start: 0.7577 (pt0) cc_final: 0.7310 (pt0) REVERT: A 212 GLU cc_start: 0.8029 (tt0) cc_final: 0.7753 (tt0) REVERT: A 233 ILE cc_start: 0.8441 (mp) cc_final: 0.8197 (mp) REVERT: A 236 ARG cc_start: 0.7533 (mtt-85) cc_final: 0.7196 (mtt-85) REVERT: A 256 GLU cc_start: 0.7459 (tp30) cc_final: 0.7232 (tp30) REVERT: A 270 LYS cc_start: 0.7374 (ptmm) cc_final: 0.6128 (ttmt) REVERT: A 281 ASN cc_start: 0.8418 (m-40) cc_final: 0.8128 (m110) REVERT: A 320 SER cc_start: 0.8406 (t) cc_final: 0.8187 (t) REVERT: H 25 CYS cc_start: 0.4530 (t) cc_final: 0.4058 (t) REVERT: H 49 GLU cc_start: 0.7493 (tt0) cc_final: 0.7179 (tt0) REVERT: H 57 TYR cc_start: 0.8835 (t80) cc_final: 0.8612 (t80) REVERT: H 76 ASP cc_start: 0.8798 (t0) cc_final: 0.8409 (t0) REVERT: H 83 TYR cc_start: 0.7367 (m-80) cc_final: 0.6970 (m-80) REVERT: L 19 ARG cc_start: 0.8584 (tpp80) cc_final: 0.8362 (mmm-85) REVERT: L 28 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7230 (tm-30) REVERT: L 38 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8185 (tm-30) REVERT: L 46 LYS cc_start: 0.8162 (pttm) cc_final: 0.7868 (pttm) REVERT: L 62 ARG cc_start: 0.7270 (ptm-80) cc_final: 0.6686 (ptt180) REVERT: L 88 TYR cc_start: 0.7457 (m-80) cc_final: 0.7207 (m-10) REVERT: L 90 GLN cc_start: 0.8080 (pp30) cc_final: 0.7774 (pt0) REVERT: R 150 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.7029 (mtm-85) REVERT: R 207 LEU cc_start: 0.8761 (mt) cc_final: 0.8405 (mt) REVERT: R 208 PHE cc_start: 0.8114 (t80) cc_final: 0.7619 (t80) REVERT: R 214 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7958 (mtt180) REVERT: R 241 TRP cc_start: 0.7109 (m-10) cc_final: 0.6720 (m-10) REVERT: R 337 MET cc_start: 0.4441 (ttp) cc_final: 0.4209 (ttp) REVERT: R 352 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7900 (mm) REVERT: R 356 TRP cc_start: 0.7033 (m-90) cc_final: 0.6284 (m-90) REVERT: R 385 LEU cc_start: 0.8376 (mt) cc_final: 0.8087 (mt) REVERT: R 409 ARG cc_start: 0.6800 (mmp-170) cc_final: 0.6578 (mmm160) outliers start: 34 outliers final: 23 residues processed: 270 average time/residue: 0.2191 time to fit residues: 75.5927 Evaluate side-chains 276 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 250 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7070 Z= 0.264 Angle : 0.748 12.433 9603 Z= 0.367 Chirality : 0.045 0.212 1106 Planarity : 0.005 0.074 1187 Dihedral : 7.677 85.249 982 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 6.46 % Allowed : 24.67 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.28), residues: 854 helix: 0.70 (0.32), residues: 256 sheet: 0.26 (0.33), residues: 236 loop : -1.49 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP L 36 HIS 0.006 0.001 HIS R 304 PHE 0.052 0.002 PHE A 244 TYR 0.024 0.002 TYR A 238 ARG 0.005 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 257 time to evaluate : 0.772 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: A 10 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7200 (ttpt) REVERT: A 17 LYS cc_start: 0.7760 (tttt) cc_final: 0.7252 (tttp) REVERT: A 29 ASP cc_start: 0.7478 (t0) cc_final: 0.7165 (t0) REVERT: A 48 LEU cc_start: 0.7010 (mp) cc_final: 0.6519 (mp) REVERT: A 49 LYS cc_start: 0.8261 (mmpt) cc_final: 0.7883 (mmpt) REVERT: A 61 PHE cc_start: 0.7016 (t80) cc_final: 0.6652 (t80) REVERT: A 62 ARG cc_start: 0.6775 (ptm160) cc_final: 0.6274 (ttt-90) REVERT: A 104 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7936 (tt) REVERT: A 106 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8580 (ttmt) REVERT: A 128 THR cc_start: 0.8252 (m) cc_final: 0.7790 (p) REVERT: A 145 GLU cc_start: 0.6424 (tm-30) cc_final: 0.5616 (tm-30) REVERT: A 147 LYS cc_start: 0.7206 (ttpt) cc_final: 0.6635 (tppt) REVERT: A 156 GLU cc_start: 0.6719 (tm-30) cc_final: 0.5952 (tm-30) REVERT: A 169 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6207 (pmt-80) REVERT: A 176 GLU cc_start: 0.7309 (pm20) cc_final: 0.6975 (pm20) REVERT: A 177 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7187 (ttp80) REVERT: A 204 ASP cc_start: 0.7473 (t0) cc_final: 0.7152 (m-30) REVERT: A 212 GLU cc_start: 0.8058 (tt0) cc_final: 0.7780 (tt0) REVERT: A 236 ARG cc_start: 0.7608 (mtt-85) cc_final: 0.7302 (mtt-85) REVERT: A 237 GLN cc_start: 0.7472 (tt0) cc_final: 0.7113 (tt0) REVERT: A 255 MET cc_start: 0.7268 (tpt) cc_final: 0.6591 (tpt) REVERT: A 256 GLU cc_start: 0.7669 (tp30) cc_final: 0.7159 (tp30) REVERT: A 257 GLU cc_start: 0.7319 (mp0) cc_final: 0.6421 (mp0) REVERT: A 270 LYS cc_start: 0.7690 (ptmm) cc_final: 0.6045 (ttpp) REVERT: A 281 ASN cc_start: 0.8424 (m-40) cc_final: 0.8056 (m-40) REVERT: A 289 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8047 (pp) REVERT: H 49 GLU cc_start: 0.7574 (tt0) cc_final: 0.7255 (tt0) REVERT: H 76 ASP cc_start: 0.8837 (t0) cc_final: 0.8312 (t0) REVERT: H 83 TYR cc_start: 0.7483 (m-80) cc_final: 0.6979 (m-80) REVERT: L 5 MET cc_start: 0.7333 (ttt) cc_final: 0.7072 (ttt) REVERT: L 19 ARG cc_start: 0.8629 (tpp80) cc_final: 0.8420 (mmm-85) REVERT: L 28 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7399 (tm-30) REVERT: L 38 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8124 (tm-30) REVERT: L 39 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7885 (tm-30) REVERT: L 46 LYS cc_start: 0.8141 (pttm) cc_final: 0.7828 (pttm) REVERT: L 62 ARG cc_start: 0.7453 (ptm-80) cc_final: 0.6823 (ptt180) REVERT: L 67 ARG cc_start: 0.7847 (ptm160) cc_final: 0.7527 (ptm160) REVERT: L 88 TYR cc_start: 0.7454 (m-80) cc_final: 0.7250 (m-10) REVERT: L 90 GLN cc_start: 0.8078 (pp30) cc_final: 0.7332 (pp30) REVERT: R 147 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5612 (tp) REVERT: R 150 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7139 (mtm-85) REVERT: R 193 LEU cc_start: 0.8591 (pp) cc_final: 0.8374 (pp) REVERT: R 208 PHE cc_start: 0.8113 (t80) cc_final: 0.7616 (t80) REVERT: R 214 ARG cc_start: 0.8406 (mtt180) cc_final: 0.7951 (mtt180) REVERT: R 241 TRP cc_start: 0.7153 (m-10) cc_final: 0.6788 (m-10) REVERT: R 337 MET cc_start: 0.4430 (ttp) cc_final: 0.4183 (ttp) REVERT: R 352 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7953 (mm) REVERT: R 356 TRP cc_start: 0.7136 (m-90) cc_final: 0.6478 (m-90) REVERT: R 385 LEU cc_start: 0.8331 (mt) cc_final: 0.8021 (mt) REVERT: R 386 CYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7109 (t) REVERT: R 409 ARG cc_start: 0.6929 (mmp-170) cc_final: 0.6697 (mmm160) outliers start: 49 outliers final: 33 residues processed: 282 average time/residue: 0.2200 time to fit residues: 78.9711 Evaluate side-chains 303 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 264 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 386 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN R 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7070 Z= 0.218 Angle : 0.739 13.345 9603 Z= 0.360 Chirality : 0.045 0.229 1106 Planarity : 0.004 0.064 1187 Dihedral : 7.525 83.936 982 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.67 % Allowed : 26.91 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.29), residues: 854 helix: 0.75 (0.32), residues: 257 sheet: 0.35 (0.33), residues: 234 loop : -1.56 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP L 36 HIS 0.005 0.001 HIS R 304 PHE 0.054 0.002 PHE A 244 TYR 0.025 0.001 TYR A 238 ARG 0.005 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 260 time to evaluate : 0.785 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: A 10 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7165 (ttpt) REVERT: A 29 ASP cc_start: 0.7460 (t0) cc_final: 0.7152 (t0) REVERT: A 61 PHE cc_start: 0.7025 (t80) cc_final: 0.6701 (t80) REVERT: A 103 ARG cc_start: 0.7179 (tpp80) cc_final: 0.6726 (tpp80) REVERT: A 104 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 106 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8575 (ttmt) REVERT: A 128 THR cc_start: 0.8253 (m) cc_final: 0.7818 (p) REVERT: A 145 GLU cc_start: 0.6408 (tm-30) cc_final: 0.5619 (tm-30) REVERT: A 147 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6633 (tppt) REVERT: A 156 GLU cc_start: 0.6623 (tm-30) cc_final: 0.5922 (tm-30) REVERT: A 169 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6240 (pmt-80) REVERT: A 176 GLU cc_start: 0.7389 (pm20) cc_final: 0.7028 (pm20) REVERT: A 177 ARG cc_start: 0.7441 (ttp80) cc_final: 0.7104 (ttp80) REVERT: A 185 GLU cc_start: 0.7465 (pt0) cc_final: 0.7240 (pt0) REVERT: A 204 ASP cc_start: 0.7220 (t0) cc_final: 0.6905 (m-30) REVERT: A 212 GLU cc_start: 0.8040 (tt0) cc_final: 0.7750 (tt0) REVERT: A 236 ARG cc_start: 0.7601 (mtt-85) cc_final: 0.7283 (mtt-85) REVERT: A 255 MET cc_start: 0.7013 (tpt) cc_final: 0.6526 (tpt) REVERT: A 256 GLU cc_start: 0.7633 (tp30) cc_final: 0.7075 (tp30) REVERT: A 257 GLU cc_start: 0.7219 (mp0) cc_final: 0.6082 (mp0) REVERT: A 270 LYS cc_start: 0.7632 (ptmm) cc_final: 0.6636 (tttm) REVERT: A 281 ASN cc_start: 0.8391 (m-40) cc_final: 0.7994 (m-40) REVERT: A 289 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8024 (pp) REVERT: H 49 GLU cc_start: 0.7537 (tt0) cc_final: 0.7242 (tt0) REVERT: H 57 TYR cc_start: 0.8827 (t80) cc_final: 0.8520 (t80) REVERT: H 76 ASP cc_start: 0.8836 (t0) cc_final: 0.8370 (t0) REVERT: H 83 TYR cc_start: 0.7480 (m-80) cc_final: 0.6905 (m-80) REVERT: L 5 MET cc_start: 0.7435 (ttt) cc_final: 0.7146 (ttt) REVERT: L 19 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8405 (mmm-85) REVERT: L 28 GLN cc_start: 0.7764 (tm130) cc_final: 0.7473 (tm-30) REVERT: L 38 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8123 (tm-30) REVERT: L 46 LYS cc_start: 0.8170 (pttm) cc_final: 0.7863 (pttm) REVERT: L 62 ARG cc_start: 0.7509 (ptm-80) cc_final: 0.6855 (ptt180) REVERT: L 67 ARG cc_start: 0.7884 (ptm160) cc_final: 0.7545 (ptm160) REVERT: L 90 GLN cc_start: 0.7972 (pp30) cc_final: 0.7237 (pp30) REVERT: R 147 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5587 (tp) REVERT: R 150 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7105 (mtm-85) REVERT: R 193 LEU cc_start: 0.8591 (pp) cc_final: 0.8350 (pp) REVERT: R 207 LEU cc_start: 0.8786 (mt) cc_final: 0.8490 (mt) REVERT: R 208 PHE cc_start: 0.8118 (t80) cc_final: 0.7598 (t80) REVERT: R 214 ARG cc_start: 0.8407 (mtt180) cc_final: 0.7945 (mtt180) REVERT: R 241 TRP cc_start: 0.7138 (m-10) cc_final: 0.6771 (m-10) REVERT: R 337 MET cc_start: 0.4426 (ttp) cc_final: 0.4187 (ttp) REVERT: R 352 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8033 (mm) REVERT: R 356 TRP cc_start: 0.7073 (m-90) cc_final: 0.6463 (m-90) REVERT: R 385 LEU cc_start: 0.8314 (mt) cc_final: 0.8082 (mt) outliers start: 43 outliers final: 30 residues processed: 278 average time/residue: 0.2185 time to fit residues: 77.2394 Evaluate side-chains 288 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7070 Z= 0.206 Angle : 0.751 13.530 9603 Z= 0.364 Chirality : 0.045 0.226 1106 Planarity : 0.005 0.063 1187 Dihedral : 7.447 83.300 982 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.41 % Allowed : 27.84 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.29), residues: 854 helix: 0.83 (0.33), residues: 251 sheet: 0.43 (0.33), residues: 232 loop : -1.52 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP L 36 HIS 0.005 0.001 HIS R 304 PHE 0.056 0.002 PHE A 244 TYR 0.025 0.001 TYR A 238 ARG 0.005 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 255 time to evaluate : 0.764 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: A 10 LYS cc_start: 0.7771 (ttpt) cc_final: 0.7175 (ttpt) REVERT: A 29 ASP cc_start: 0.7458 (t0) cc_final: 0.7140 (t0) REVERT: A 59 CYS cc_start: 0.7963 (t) cc_final: 0.7497 (p) REVERT: A 61 PHE cc_start: 0.7034 (t80) cc_final: 0.6743 (t80) REVERT: A 103 ARG cc_start: 0.7156 (tpp80) cc_final: 0.6721 (tpp80) REVERT: A 104 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 106 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8590 (ttmt) REVERT: A 145 GLU cc_start: 0.6414 (tm-30) cc_final: 0.5748 (tm-30) REVERT: A 147 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6631 (tppt) REVERT: A 156 GLU cc_start: 0.6642 (tm-30) cc_final: 0.5922 (tm-30) REVERT: A 176 GLU cc_start: 0.7484 (pm20) cc_final: 0.7193 (pm20) REVERT: A 177 ARG cc_start: 0.7470 (ttp80) cc_final: 0.7104 (ttp80) REVERT: A 185 GLU cc_start: 0.7446 (pt0) cc_final: 0.7227 (pt0) REVERT: A 204 ASP cc_start: 0.7278 (t0) cc_final: 0.6936 (m-30) REVERT: A 212 GLU cc_start: 0.8045 (tt0) cc_final: 0.7749 (tt0) REVERT: A 236 ARG cc_start: 0.7627 (mtt-85) cc_final: 0.7330 (mtt-85) REVERT: A 255 MET cc_start: 0.7026 (tpt) cc_final: 0.6707 (tpt) REVERT: A 256 GLU cc_start: 0.7586 (tp30) cc_final: 0.7098 (tp30) REVERT: A 257 GLU cc_start: 0.7259 (mp0) cc_final: 0.6271 (mp0) REVERT: A 270 LYS cc_start: 0.7590 (ptmm) cc_final: 0.5829 (tmtt) REVERT: A 281 ASN cc_start: 0.8422 (m-40) cc_final: 0.8147 (m110) REVERT: H 49 GLU cc_start: 0.7553 (tt0) cc_final: 0.7239 (tt0) REVERT: H 57 TYR cc_start: 0.8869 (t80) cc_final: 0.8523 (t80) REVERT: H 76 ASP cc_start: 0.8805 (t0) cc_final: 0.8447 (t0) REVERT: H 83 TYR cc_start: 0.7470 (m-80) cc_final: 0.6907 (m-80) REVERT: L 5 MET cc_start: 0.7428 (ttt) cc_final: 0.7185 (ttt) REVERT: L 19 ARG cc_start: 0.8619 (tpp80) cc_final: 0.8408 (mmm-85) REVERT: L 38 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8169 (tm-30) REVERT: L 46 LYS cc_start: 0.8199 (pttm) cc_final: 0.7897 (pttm) REVERT: L 62 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6940 (ptt180) REVERT: L 90 GLN cc_start: 0.7886 (pp30) cc_final: 0.7195 (pp30) REVERT: R 147 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5758 (tp) REVERT: R 193 LEU cc_start: 0.8555 (pp) cc_final: 0.8318 (pp) REVERT: R 207 LEU cc_start: 0.8798 (mt) cc_final: 0.8511 (mt) REVERT: R 208 PHE cc_start: 0.8083 (t80) cc_final: 0.7569 (t80) REVERT: R 214 ARG cc_start: 0.8394 (mtt180) cc_final: 0.7930 (mtt180) REVERT: R 241 TRP cc_start: 0.7166 (m-10) cc_final: 0.6809 (m-10) REVERT: R 337 MET cc_start: 0.4434 (ttp) cc_final: 0.4186 (ttp) REVERT: R 352 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8027 (mm) REVERT: R 356 TRP cc_start: 0.7050 (m-90) cc_final: 0.6426 (m-90) REVERT: R 385 LEU cc_start: 0.8423 (mt) cc_final: 0.8132 (mt) outliers start: 41 outliers final: 31 residues processed: 272 average time/residue: 0.2172 time to fit residues: 75.5186 Evaluate side-chains 290 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 255 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 129 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7070 Z= 0.211 Angle : 0.754 12.300 9603 Z= 0.366 Chirality : 0.045 0.228 1106 Planarity : 0.005 0.077 1187 Dihedral : 7.370 82.753 982 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.80 % Allowed : 27.44 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.29), residues: 854 helix: 0.83 (0.33), residues: 257 sheet: 0.44 (0.33), residues: 235 loop : -1.57 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP L 36 HIS 0.005 0.001 HIS R 304 PHE 0.058 0.002 PHE A 244 TYR 0.027 0.002 TYR L 88 ARG 0.011 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 252 time to evaluate : 0.781 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: A 10 LYS cc_start: 0.7787 (ttpt) cc_final: 0.7175 (ttpt) REVERT: A 24 LYS cc_start: 0.8482 (pttm) cc_final: 0.8201 (pttm) REVERT: A 29 ASP cc_start: 0.7447 (t0) cc_final: 0.7117 (t0) REVERT: A 50 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: A 61 PHE cc_start: 0.7033 (t80) cc_final: 0.6729 (t80) REVERT: A 103 ARG cc_start: 0.7175 (tpp80) cc_final: 0.6721 (tpp80) REVERT: A 104 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7837 (tt) REVERT: A 106 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8592 (ttmt) REVERT: A 145 GLU cc_start: 0.6359 (tm-30) cc_final: 0.5630 (tm-30) REVERT: A 147 LYS cc_start: 0.7232 (ttpt) cc_final: 0.6652 (tppt) REVERT: A 156 GLU cc_start: 0.6641 (tm-30) cc_final: 0.5933 (tm-30) REVERT: A 176 GLU cc_start: 0.7532 (pm20) cc_final: 0.6933 (pm20) REVERT: A 177 ARG cc_start: 0.7465 (ttp80) cc_final: 0.7089 (ttp80) REVERT: A 203 LEU cc_start: 0.7313 (mm) cc_final: 0.7031 (mt) REVERT: A 204 ASP cc_start: 0.7204 (t0) cc_final: 0.6868 (m-30) REVERT: A 212 GLU cc_start: 0.8045 (tt0) cc_final: 0.7731 (tt0) REVERT: A 236 ARG cc_start: 0.7637 (mtt-85) cc_final: 0.7391 (mtt-85) REVERT: A 255 MET cc_start: 0.7437 (tpt) cc_final: 0.7098 (tpt) REVERT: A 256 GLU cc_start: 0.7555 (tp30) cc_final: 0.7178 (tp30) REVERT: A 257 GLU cc_start: 0.7252 (mp0) cc_final: 0.6335 (mp0) REVERT: A 270 LYS cc_start: 0.7589 (ptmm) cc_final: 0.5809 (tmtt) REVERT: A 281 ASN cc_start: 0.8394 (m-40) cc_final: 0.8084 (m-40) REVERT: A 355 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7665 (mtmt) REVERT: H 49 GLU cc_start: 0.7543 (tt0) cc_final: 0.7231 (tt0) REVERT: H 50 TRP cc_start: 0.8325 (t60) cc_final: 0.8026 (t60) REVERT: H 57 TYR cc_start: 0.8870 (t80) cc_final: 0.8498 (t80) REVERT: H 76 ASP cc_start: 0.8837 (t0) cc_final: 0.8362 (t0) REVERT: H 83 TYR cc_start: 0.7501 (m-80) cc_final: 0.6918 (m-80) REVERT: L 5 MET cc_start: 0.7459 (ttt) cc_final: 0.7231 (ttt) REVERT: L 19 ARG cc_start: 0.8628 (tpp80) cc_final: 0.8415 (mmm-85) REVERT: L 38 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8095 (tm-30) REVERT: L 46 LYS cc_start: 0.8192 (pttm) cc_final: 0.7882 (pttm) REVERT: L 56 TYR cc_start: 0.7885 (t80) cc_final: 0.7542 (t80) REVERT: L 62 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6984 (ptt180) REVERT: L 90 GLN cc_start: 0.7921 (pp30) cc_final: 0.7227 (pp30) REVERT: R 150 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7477 (mtm-85) REVERT: R 193 LEU cc_start: 0.8554 (pp) cc_final: 0.8316 (pp) REVERT: R 208 PHE cc_start: 0.8072 (t80) cc_final: 0.7550 (t80) REVERT: R 214 ARG cc_start: 0.8373 (mtt180) cc_final: 0.7915 (mtt180) REVERT: R 241 TRP cc_start: 0.7167 (m-10) cc_final: 0.6790 (m-10) REVERT: R 337 MET cc_start: 0.4456 (ttp) cc_final: 0.4226 (ttp) REVERT: R 352 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8055 (mm) REVERT: R 356 TRP cc_start: 0.7013 (m-90) cc_final: 0.6388 (m-90) REVERT: R 385 LEU cc_start: 0.8444 (mt) cc_final: 0.8142 (mt) outliers start: 44 outliers final: 33 residues processed: 271 average time/residue: 0.2376 time to fit residues: 82.8772 Evaluate side-chains 288 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 129 PHE Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.0020 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7070 Z= 0.194 Angle : 0.765 12.559 9603 Z= 0.368 Chirality : 0.045 0.219 1106 Planarity : 0.004 0.071 1187 Dihedral : 7.249 82.297 982 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.28 % Allowed : 28.36 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.29), residues: 854 helix: 0.96 (0.33), residues: 251 sheet: 0.57 (0.33), residues: 233 loop : -1.58 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP L 36 HIS 0.005 0.001 HIS R 304 PHE 0.054 0.002 PHE A 244 TYR 0.025 0.001 TYR A 238 ARG 0.006 0.000 ARG R 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 255 time to evaluate : 0.745 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: A 10 LYS cc_start: 0.7771 (ttpt) cc_final: 0.7164 (ttpt) REVERT: A 24 LYS cc_start: 0.8499 (pttm) cc_final: 0.8216 (pttm) REVERT: A 29 ASP cc_start: 0.7384 (t0) cc_final: 0.7064 (t0) REVERT: A 50 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: A 61 PHE cc_start: 0.7013 (t80) cc_final: 0.6750 (t80) REVERT: A 103 ARG cc_start: 0.7172 (tpp80) cc_final: 0.6709 (tpp80) REVERT: A 104 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7803 (tt) REVERT: A 106 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8577 (ttmt) REVERT: A 145 GLU cc_start: 0.6401 (tm-30) cc_final: 0.5859 (tm-30) REVERT: A 147 LYS cc_start: 0.7229 (ttpt) cc_final: 0.6654 (tppt) REVERT: A 156 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6021 (tm-30) REVERT: A 176 GLU cc_start: 0.7535 (pm20) cc_final: 0.6953 (pm20) REVERT: A 177 ARG cc_start: 0.7432 (ttp80) cc_final: 0.7110 (ttp80) REVERT: A 185 GLU cc_start: 0.7426 (pt0) cc_final: 0.7214 (pt0) REVERT: A 203 LEU cc_start: 0.7293 (mm) cc_final: 0.7000 (mt) REVERT: A 204 ASP cc_start: 0.7162 (t0) cc_final: 0.6856 (m-30) REVERT: A 212 GLU cc_start: 0.8039 (tt0) cc_final: 0.7714 (tt0) REVERT: A 255 MET cc_start: 0.7393 (tpt) cc_final: 0.7156 (tpt) REVERT: A 257 GLU cc_start: 0.7153 (mp0) cc_final: 0.6493 (mp0) REVERT: A 270 LYS cc_start: 0.7466 (ptmm) cc_final: 0.6040 (ttmt) REVERT: A 271 VAL cc_start: 0.8656 (t) cc_final: 0.8287 (m) REVERT: A 281 ASN cc_start: 0.8367 (m-40) cc_final: 0.8094 (m-40) REVERT: A 355 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7648 (mtmt) REVERT: H 49 GLU cc_start: 0.7525 (tt0) cc_final: 0.7227 (tt0) REVERT: H 50 TRP cc_start: 0.8320 (t60) cc_final: 0.8013 (t60) REVERT: H 57 TYR cc_start: 0.8866 (t80) cc_final: 0.8444 (t80) REVERT: H 76 ASP cc_start: 0.8837 (t0) cc_final: 0.8474 (t0) REVERT: H 83 TYR cc_start: 0.7497 (m-80) cc_final: 0.6828 (m-80) REVERT: L 19 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8413 (mmm-85) REVERT: L 38 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8034 (tm-30) REVERT: L 46 LYS cc_start: 0.8170 (pttm) cc_final: 0.7890 (pttm) REVERT: L 56 TYR cc_start: 0.7863 (t80) cc_final: 0.7506 (t80) REVERT: L 62 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7007 (ptt180) REVERT: L 90 GLN cc_start: 0.7887 (pp30) cc_final: 0.7258 (pp30) REVERT: R 150 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7308 (mtm-85) REVERT: R 193 LEU cc_start: 0.8509 (pp) cc_final: 0.8278 (pp) REVERT: R 208 PHE cc_start: 0.8079 (t80) cc_final: 0.7591 (t80) REVERT: R 214 ARG cc_start: 0.8335 (mtt180) cc_final: 0.7888 (mtt180) REVERT: R 241 TRP cc_start: 0.7175 (m-10) cc_final: 0.6793 (m-10) REVERT: R 337 MET cc_start: 0.4513 (ttp) cc_final: 0.4275 (ttp) REVERT: R 352 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8126 (mm) REVERT: R 356 TRP cc_start: 0.6917 (m-90) cc_final: 0.6283 (m-90) REVERT: R 385 LEU cc_start: 0.8372 (mt) cc_final: 0.8099 (mt) outliers start: 40 outliers final: 32 residues processed: 271 average time/residue: 0.2186 time to fit residues: 75.1240 Evaluate side-chains 286 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 250 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 69 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.164900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.138795 restraints weight = 14357.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.143235 restraints weight = 7860.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.146114 restraints weight = 5135.681| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7070 Z= 0.206 Angle : 0.768 12.456 9603 Z= 0.373 Chirality : 0.045 0.217 1106 Planarity : 0.005 0.065 1187 Dihedral : 7.231 81.913 982 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.01 % Allowed : 28.50 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.29), residues: 854 helix: 1.00 (0.33), residues: 250 sheet: 0.54 (0.33), residues: 234 loop : -1.50 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP L 36 HIS 0.005 0.001 HIS R 304 PHE 0.054 0.002 PHE A 244 TYR 0.025 0.001 TYR A 238 ARG 0.012 0.000 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.04 seconds wall clock time: 38 minutes 16.77 seconds (2296.77 seconds total)