Starting phenix.real_space_refine on Wed Jan 17 20:28:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/01_2024/8qjy_18454.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/01_2024/8qjy_18454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/01_2024/8qjy_18454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/01_2024/8qjy_18454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/01_2024/8qjy_18454.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/01_2024/8qjy_18454.pdb" } resolution = 3.5 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3961 2.51 5 N 1044 2.21 5 O 1252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6287 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1643 Classifications: {'peptide': 207} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 199} Chain breaks: 2 Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Time building chain proxies: 3.93, per 1000 atoms: 0.63 Number of scatterers: 6287 At special positions: 0 Unit cell: (94.9, 101.4, 98.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1252 8.00 N 1044 7.00 C 3961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1526 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 13 sheets defined 9.4% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 249 through 252 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.922A pdb=" N PHE A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 5.227A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 246 through 252 removed outlier: 5.482A pdb=" N LYS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.537A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU D 191 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE D 151 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.623A pdb=" N LEU D 128 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR D 173 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 222 through 223 removed outlier: 6.704A pdb=" N VAL D 285 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG D 243 " --> pdb=" O GLY D 283 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY D 283 " --> pdb=" O ARG D 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 229 through 233 removed outlier: 6.543A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AA6, first strand: chain 'C' and resid 190 through 199 removed outlier: 5.780A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 218 through 220 removed outlier: 4.574A pdb=" N HIS C 218 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 199 removed outlier: 6.389A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 218 through 220 removed outlier: 4.584A pdb=" N HIS A 218 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 199 removed outlier: 6.417A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 218 through 220 removed outlier: 4.414A pdb=" N HIS B 218 " --> pdb=" O ALA B 225 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 489 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: 1.60 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2054 1.35 - 1.46: 1550 1.46 - 1.58: 2762 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 6414 Sorted by residual: bond pdb=" N MET C 276 " pdb=" CA MET C 276 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.18e+00 bond pdb=" N ARG C 279 " pdb=" CA ARG C 279 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.40e-02 5.10e+03 5.50e+00 bond pdb=" N ARG C 280 " pdb=" CA ARG C 280 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.16e-02 7.43e+03 5.40e+00 bond pdb=" C ARG C 280 " pdb=" O ARG C 280 " ideal model delta sigma weight residual 1.235 1.249 -0.014 1.25e-02 6.40e+03 1.26e+00 bond pdb=" C ASN A 278 " pdb=" O ASN A 278 " ideal model delta sigma weight residual 1.243 1.233 0.010 9.50e-03 1.11e+04 1.14e+00 ... (remaining 6409 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.05: 171 107.05 - 113.79: 3602 113.79 - 120.53: 2362 120.53 - 127.27: 2547 127.27 - 134.01: 58 Bond angle restraints: 8740 Sorted by residual: angle pdb=" C MET C 276 " pdb=" N LEU C 277 " pdb=" CA LEU C 277 " ideal model delta sigma weight residual 122.82 112.34 10.48 2.12e+00 2.22e-01 2.45e+01 angle pdb=" C ASN B 278 " pdb=" CA ASN B 278 " pdb=" CB ASN B 278 " ideal model delta sigma weight residual 116.54 111.22 5.32 1.15e+00 7.56e-01 2.14e+01 angle pdb=" N ARG C 279 " pdb=" CA ARG C 279 " pdb=" C ARG C 279 " ideal model delta sigma weight residual 113.89 107.05 6.84 1.58e+00 4.01e-01 1.87e+01 angle pdb=" C ASN A 278 " pdb=" CA ASN A 278 " pdb=" CB ASN A 278 " ideal model delta sigma weight residual 117.23 111.43 5.80 1.36e+00 5.41e-01 1.82e+01 angle pdb=" N ARG B 279 " pdb=" CA ARG B 279 " pdb=" CB ARG B 279 " ideal model delta sigma weight residual 114.17 109.44 4.73 1.14e+00 7.69e-01 1.72e+01 ... (remaining 8735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 3469 17.38 - 34.77: 287 34.77 - 52.15: 50 52.15 - 69.54: 6 69.54 - 86.92: 7 Dihedral angle restraints: 3819 sinusoidal: 1466 harmonic: 2353 Sorted by residual: dihedral pdb=" CA VAL A 138 " pdb=" C VAL A 138 " pdb=" N ASN A 139 " pdb=" CA ASN A 139 " ideal model delta harmonic sigma weight residual 180.00 -162.26 -17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA LEU B 212 " pdb=" C LEU B 212 " pdb=" N LYS B 213 " pdb=" CA LYS B 213 " ideal model delta harmonic sigma weight residual 180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB GLU B 196 " pdb=" CG GLU B 196 " pdb=" CD GLU B 196 " pdb=" OE1 GLU B 196 " ideal model delta sinusoidal sigma weight residual 0.00 -86.92 86.92 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 3816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 662 0.036 - 0.073: 253 0.073 - 0.109: 62 0.109 - 0.146: 42 0.146 - 0.182: 2 Chirality restraints: 1021 Sorted by residual: chirality pdb=" CA MET C 276 " pdb=" N MET C 276 " pdb=" C MET C 276 " pdb=" CB MET C 276 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA ILE C 255 " pdb=" N ILE C 255 " pdb=" C ILE C 255 " pdb=" CB ILE C 255 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE B 176 " pdb=" N ILE B 176 " pdb=" C ILE B 176 " pdb=" CB ILE B 176 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 1018 not shown) Planarity restraints: 1123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 324 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO D 325 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 325 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 325 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 139 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 140 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 249 " -0.143 9.50e-02 1.11e+02 6.45e-02 2.82e+00 pdb=" NE ARG C 249 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 249 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 249 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 249 " -0.002 2.00e-02 2.50e+03 ... (remaining 1120 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 15 2.33 - 2.97: 3327 2.97 - 3.61: 8897 3.61 - 4.26: 14822 4.26 - 4.90: 24942 Nonbonded interactions: 52003 Sorted by model distance: nonbonded pdb=" OH TYR C 254 " pdb=" NH2 ARG C 279 " model vdw 1.682 2.520 nonbonded pdb=" O ASN A 192 " pdb=" ND2 ASN A 192 " model vdw 1.908 2.520 nonbonded pdb=" OH TYR C 319 " pdb=" OH TYR A 319 " model vdw 1.921 2.440 nonbonded pdb=" OD1 ASN C 278 " pdb=" N CYS C 289 " model vdw 1.988 2.520 nonbonded pdb=" OH TYR C 319 " pdb=" OH TYR B 319 " model vdw 2.020 2.440 ... (remaining 51998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.270 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.300 Find NCS groups from input model: 0.350 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.003 0.035 6414 Z= 0.207 Angle : 0.607 10.483 8740 Z= 0.364 Chirality : 0.046 0.182 1021 Planarity : 0.004 0.064 1123 Dihedral : 13.674 86.923 2293 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.14 % Allowed : 16.74 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.59 (0.31), residues: 786 helix: -0.85 (1.16), residues: 18 sheet: -0.53 (0.27), residues: 322 loop : -0.14 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 296 HIS 0.005 0.001 HIS B 218 PHE 0.022 0.002 PHE D 301 TYR 0.012 0.002 TYR C 174 ARG 0.009 0.001 ARG C 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 299 LEU cc_start: 0.8127 (mt) cc_final: 0.7904 (mp) REVERT: A 222 GLN cc_start: 0.7904 (mm110) cc_final: 0.7618 (mm110) REVERT: A 236 MET cc_start: 0.8374 (mmp) cc_final: 0.7800 (mmt) REVERT: B 252 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7424 (mt-10) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.2517 time to fit residues: 65.4268 Evaluate side-chains 136 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6414 Z= 0.202 Angle : 0.615 6.937 8740 Z= 0.322 Chirality : 0.046 0.136 1021 Planarity : 0.004 0.045 1123 Dihedral : 4.681 16.637 860 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.94 % Allowed : 17.44 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.04 (0.32), residues: 786 helix: -0.73 (1.22), residues: 18 sheet: 0.06 (0.30), residues: 291 loop : 0.05 (0.32), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 296 HIS 0.005 0.001 HIS B 218 PHE 0.018 0.002 PHE D 247 TYR 0.015 0.002 TYR D 172 ARG 0.005 0.001 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 0.766 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: D 172 TYR cc_start: 0.6956 (m-80) cc_final: 0.6165 (m-80) REVERT: A 222 GLN cc_start: 0.8029 (mm110) cc_final: 0.7780 (mm110) REVERT: B 158 LEU cc_start: 0.8757 (tp) cc_final: 0.8490 (tp) REVERT: B 233 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8463 (ttpp) outliers start: 28 outliers final: 16 residues processed: 155 average time/residue: 0.2096 time to fit residues: 41.4393 Evaluate side-chains 140 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 284 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 8.9990 chunk 21 optimal weight: 0.1980 chunk 58 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS C 283 ASN A 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6414 Z= 0.204 Angle : 0.569 6.587 8740 Z= 0.298 Chirality : 0.044 0.132 1021 Planarity : 0.004 0.039 1123 Dihedral : 4.517 16.025 860 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.94 % Allowed : 17.30 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.03 (0.32), residues: 786 helix: -0.03 (1.33), residues: 18 sheet: 0.11 (0.30), residues: 297 loop : 0.07 (0.32), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 296 HIS 0.008 0.001 HIS D 183 PHE 0.019 0.002 PHE C 193 TYR 0.019 0.001 TYR D 293 ARG 0.006 0.001 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.8277 (ppp) cc_final: 0.7920 (ppp) REVERT: A 222 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7889 (mm110) REVERT: B 158 LEU cc_start: 0.8732 (tp) cc_final: 0.8490 (tp) REVERT: B 256 TYR cc_start: 0.8604 (m-80) cc_final: 0.8322 (m-80) outliers start: 28 outliers final: 21 residues processed: 144 average time/residue: 0.1895 time to fit residues: 35.7630 Evaluate side-chains 140 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 279 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6414 Z= 0.396 Angle : 0.626 6.169 8740 Z= 0.333 Chirality : 0.045 0.136 1021 Planarity : 0.004 0.037 1123 Dihedral : 4.921 16.000 860 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.77 % Allowed : 17.72 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.20 (0.32), residues: 786 helix: 0.08 (1.32), residues: 18 sheet: -0.12 (0.29), residues: 312 loop : -0.04 (0.33), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 294 HIS 0.004 0.001 HIS D 312 PHE 0.021 0.002 PHE B 172 TYR 0.020 0.002 TYR A 260 ARG 0.010 0.001 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.8489 (ppp) cc_final: 0.8055 (ppp) REVERT: C 250 GLU cc_start: 0.7977 (pm20) cc_final: 0.7715 (pm20) REVERT: B 259 CYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7471 (m) outliers start: 41 outliers final: 31 residues processed: 140 average time/residue: 0.1904 time to fit residues: 35.1229 Evaluate side-chains 136 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 300 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6414 Z= 0.181 Angle : 0.563 7.406 8740 Z= 0.293 Chirality : 0.045 0.173 1021 Planarity : 0.003 0.031 1123 Dihedral : 4.576 17.888 860 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.50 % Allowed : 19.83 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.10 (0.32), residues: 786 helix: 0.27 (1.36), residues: 18 sheet: -0.02 (0.29), residues: 312 loop : -0.00 (0.33), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 296 HIS 0.002 0.001 HIS B 218 PHE 0.019 0.002 PHE C 193 TYR 0.018 0.001 TYR C 320 ARG 0.007 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 0.809 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: D 130 MET cc_start: 0.8401 (ppp) cc_final: 0.8010 (ppp) REVERT: A 236 MET cc_start: 0.8287 (mmp) cc_final: 0.7802 (mmt) REVERT: B 256 TYR cc_start: 0.8587 (m-80) cc_final: 0.8327 (m-80) outliers start: 32 outliers final: 26 residues processed: 135 average time/residue: 0.2244 time to fit residues: 39.8405 Evaluate side-chains 137 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 309 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 6414 Z= 0.563 Angle : 0.716 7.523 8740 Z= 0.384 Chirality : 0.047 0.145 1021 Planarity : 0.004 0.036 1123 Dihedral : 5.328 19.716 860 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.34 % Allowed : 20.39 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.31), residues: 786 helix: -1.43 (0.88), residues: 36 sheet: -0.18 (0.28), residues: 311 loop : -0.24 (0.33), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 294 HIS 0.004 0.002 HIS D 312 PHE 0.023 0.002 PHE B 172 TYR 0.024 0.002 TYR A 260 ARG 0.012 0.001 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 106 time to evaluate : 0.880 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: D 130 MET cc_start: 0.8611 (ppp) cc_final: 0.8097 (ppp) REVERT: C 324 ASP cc_start: 0.7580 (p0) cc_final: 0.7285 (p0) REVERT: B 164 LYS cc_start: 0.9173 (tppp) cc_final: 0.8969 (tppp) outliers start: 38 outliers final: 33 residues processed: 130 average time/residue: 0.2048 time to fit residues: 34.6509 Evaluate side-chains 131 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 309 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 165 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6414 Z= 0.170 Angle : 0.590 6.779 8740 Z= 0.307 Chirality : 0.045 0.158 1021 Planarity : 0.004 0.039 1123 Dihedral : 4.731 18.734 860 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.64 % Allowed : 22.08 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.31 (0.31), residues: 786 helix: -1.12 (0.90), residues: 36 sheet: -0.03 (0.29), residues: 312 loop : -0.14 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 296 HIS 0.003 0.001 HIS B 218 PHE 0.017 0.002 PHE A 172 TYR 0.014 0.001 TYR A 260 ARG 0.008 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 0.688 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: D 130 MET cc_start: 0.8470 (ppp) cc_final: 0.8040 (ppp) REVERT: A 164 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8217 (mtpt) REVERT: A 224 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7590 (mpp) outliers start: 33 outliers final: 28 residues processed: 136 average time/residue: 0.1797 time to fit residues: 32.0994 Evaluate side-chains 140 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 300 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 6414 Z= 0.514 Angle : 0.714 7.944 8740 Z= 0.380 Chirality : 0.046 0.146 1021 Planarity : 0.004 0.039 1123 Dihedral : 5.384 20.634 860 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.20 % Allowed : 21.38 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.60 (0.31), residues: 786 helix: -1.35 (0.87), residues: 36 sheet: -0.25 (0.28), residues: 312 loop : -0.32 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 294 HIS 0.004 0.001 HIS D 312 PHE 0.021 0.002 PHE B 172 TYR 0.024 0.002 TYR A 260 ARG 0.008 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 102 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: D 130 MET cc_start: 0.8631 (ppp) cc_final: 0.8104 (ppp) REVERT: C 324 ASP cc_start: 0.7585 (p0) cc_final: 0.7320 (p0) REVERT: A 184 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6319 (tmm) REVERT: A 224 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7666 (mpp) REVERT: A 236 MET cc_start: 0.8441 (mmp) cc_final: 0.8048 (mmt) outliers start: 37 outliers final: 31 residues processed: 126 average time/residue: 0.2029 time to fit residues: 32.9767 Evaluate side-chains 131 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 300 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6414 Z= 0.184 Angle : 0.633 7.387 8740 Z= 0.326 Chirality : 0.045 0.151 1021 Planarity : 0.004 0.049 1123 Dihedral : 4.949 24.223 860 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.22 % Allowed : 22.64 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.31), residues: 786 helix: -1.67 (0.89), residues: 36 sheet: -0.11 (0.28), residues: 312 loop : -0.36 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 296 HIS 0.003 0.001 HIS B 218 PHE 0.017 0.002 PHE A 172 TYR 0.017 0.001 TYR D 172 ARG 0.010 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.8521 (ppp) cc_final: 0.8075 (ppp) REVERT: A 164 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8436 (mtpt) REVERT: A 224 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7652 (mpp) REVERT: B 164 LYS cc_start: 0.8869 (tppp) cc_final: 0.8606 (tppt) outliers start: 30 outliers final: 23 residues processed: 130 average time/residue: 0.1873 time to fit residues: 31.8799 Evaluate side-chains 133 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 6414 Z= 0.437 Angle : 0.724 10.244 8740 Z= 0.378 Chirality : 0.045 0.159 1021 Planarity : 0.004 0.040 1123 Dihedral : 5.296 22.832 860 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.80 % Allowed : 24.19 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.82 (0.31), residues: 786 helix: -2.09 (0.66), residues: 54 sheet: -0.30 (0.28), residues: 312 loop : -0.40 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 294 HIS 0.003 0.001 HIS D 312 PHE 0.028 0.003 PHE D 247 TYR 0.022 0.002 TYR A 260 ARG 0.009 0.001 ARG B 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.753 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: D 130 MET cc_start: 0.8613 (ppp) cc_final: 0.8093 (ppp) REVERT: C 324 ASP cc_start: 0.7649 (p0) cc_final: 0.7373 (p0) REVERT: A 224 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7671 (mpp) outliers start: 27 outliers final: 25 residues processed: 124 average time/residue: 0.2080 time to fit residues: 33.2520 Evaluate side-chains 129 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 272 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 284 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.047940 restraints weight = 23362.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.049799 restraints weight = 11130.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.051079 restraints weight = 7111.156| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6414 Z= 0.228 Angle : 0.654 8.841 8740 Z= 0.337 Chirality : 0.045 0.154 1021 Planarity : 0.004 0.048 1123 Dihedral : 5.037 23.730 860 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.66 % Allowed : 24.33 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.51 (0.31), residues: 786 helix: -0.83 (0.90), residues: 36 sheet: -0.22 (0.29), residues: 312 loop : -0.27 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 296 HIS 0.003 0.001 HIS B 218 PHE 0.029 0.002 PHE D 247 TYR 0.018 0.002 TYR C 320 ARG 0.010 0.001 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1534.24 seconds wall clock time: 30 minutes 50.41 seconds (1850.41 seconds total)