Starting phenix.real_space_refine on Fri Dec 8 00:52:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/12_2023/8qjy_18454.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/12_2023/8qjy_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_18454/12_2023/8qjy_18454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/12_2023/8qjy_18454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/12_2023/8qjy_18454.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjy_18454/12_2023/8qjy_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-1.21rc1-5172/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: 4.21, per 1000 atoms: 0.67 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: 2.43 Conformation dependent library (CDL) restraints added in 1.4 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: 0.75 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: 1.83 Time building geometry restraints manager: 2.61 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: 0.150 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: 0.010 Extract box with map and model: 1.260 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.440 Find NCS groups from input model: 0.370 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.220 ------------------------------------------------------------------------------- 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 : 0.724 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 outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.2581 time to fit residues: 66.7615 Evaluate side-chains 136 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0109 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.8121 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6414 Z= 0.212 Angle : 0.617 6.811 8740 Z= 0.322 Chirality : 0.046 0.136 1021 Planarity : 0.004 0.045 1123 Dihedral : 4.678 16.339 860 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.08 % Allowed : 17.72 % Favored : 78.20 % 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: -0.65 (1.22), residues: 18 sheet: 0.07 (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 0.019 0.002 PHE D 247 TYR 0.015 0.002 TYR D 172 ARG 0.005 0.001 ARG B 322 *********************** 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 168 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 0.826 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 outliers start: 29 outliers final: 17 residues processed: 158 average time/residue: 0.2166 time to fit residues: 43.5105 Evaluate side-chains 141 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0631 time to fit residues: 3.0074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0000 chunk 58 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6414 Z= 0.162 Angle : 0.563 6.125 8740 Z= 0.293 Chirality : 0.045 0.134 1021 Planarity : 0.003 0.038 1123 Dihedral : 4.403 15.212 860 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.69 % Allowed : 17.58 % Favored : 80.73 % 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: 0.12 (0.32), residues: 786 helix: -0.01 (1.35), residues: 18 sheet: 0.23 (0.30), residues: 291 loop : 0.09 (0.32), residues: 477 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 0.021 0.001 TYR D 172 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 144 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 143 average time/residue: 0.2043 time to fit residues: 37.9914 Evaluate side-chains 123 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0675 time to fit residues: 1.5980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6414 Z= 0.296 Angle : 0.585 6.585 8740 Z= 0.309 Chirality : 0.044 0.135 1021 Planarity : 0.004 0.033 1123 Dihedral : 4.578 15.260 860 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.67 % Allowed : 19.55 % Favored : 77.78 % 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: -0.06 (0.32), residues: 786 helix: 0.34 (1.33), residues: 18 sheet: -0.02 (0.29), residues: 312 loop : 0.06 (0.33), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 296 HIS 0.003 0.001 HIS D 312 PHE 0.016 0.002 PHE B 172 TYR 0.018 0.002 TYR A 260 ARG 0.009 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 131 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 0.1971 time to fit residues: 30.9627 Evaluate side-chains 118 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0941 time to fit residues: 2.8632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.0040 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.0396 ------------------------------------------------------------------------------- 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 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4241 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= 0.169 Angle : 0.552 6.583 8740 Z= 0.290 Chirality : 0.044 0.135 1021 Planarity : 0.003 0.029 1123 Dihedral : 4.452 17.766 860 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.27 % Allowed : 20.25 % Favored : 78.48 % 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: 0.00 (0.32), residues: 786 helix: 0.33 (1.38), residues: 18 sheet: 0.10 (0.29), residues: 314 loop : 0.03 (0.33), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 296 HIS 0.002 0.001 HIS B 218 PHE 0.013 0.001 PHE C 172 TYR 0.014 0.001 TYR C 320 ARG 0.006 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 122 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 0.1955 time to fit residues: 30.5646 Evaluate side-chains 108 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0629 time to fit residues: 1.6378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 6414 Z= 0.460 Angle : 0.668 6.375 8740 Z= 0.357 Chirality : 0.045 0.141 1021 Planarity : 0.004 0.032 1123 Dihedral : 5.096 18.999 860 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.95 % Allowed : 20.11 % Favored : 76.93 % 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: -0.24 (0.31), residues: 786 helix: -0.35 (1.26), residues: 18 sheet: -0.03 (0.28), residues: 312 loop : -0.15 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 296 HIS 0.003 0.001 HIS D 312 PHE 0.021 0.002 PHE B 172 TYR 0.021 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 125 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 112 average time/residue: 0.2099 time to fit residues: 30.5415 Evaluate side-chains 115 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0607 time to fit residues: 2.9899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6414 Z= 0.185 Angle : 0.591 6.247 8740 Z= 0.308 Chirality : 0.044 0.142 1021 Planarity : 0.004 0.038 1123 Dihedral : 4.703 15.930 860 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.84 % Allowed : 20.82 % Favored : 78.34 % 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: -0.18 (0.31), residues: 786 helix: -1.34 (0.87), residues: 36 sheet: 0.10 (0.29), residues: 312 loop : -0.06 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 296 HIS 0.003 0.001 HIS B 218 PHE 0.021 0.002 PHE A 172 TYR 0.015 0.001 TYR C 320 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 121 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 117 average time/residue: 0.1937 time to fit residues: 30.2396 Evaluate side-chains 109 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0677 time to fit residues: 1.4692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 208 GLN ** 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: 0.8258 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6414 Z= 0.286 Angle : 0.636 8.335 8740 Z= 0.330 Chirality : 0.044 0.141 1021 Planarity : 0.003 0.033 1123 Dihedral : 4.791 16.256 860 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.84 % Allowed : 21.80 % Favored : 77.36 % 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: -0.18 (0.31), residues: 786 helix: 0.11 (1.33), residues: 18 sheet: 0.06 (0.29), residues: 312 loop : -0.17 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 296 HIS 0.003 0.001 HIS D 312 PHE 0.018 0.002 PHE A 172 TYR 0.021 0.002 TYR D 293 ARG 0.009 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 109 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 105 average time/residue: 0.1918 time to fit residues: 26.6855 Evaluate side-chains 106 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0594 time to fit residues: 1.4542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.0470 chunk 68 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 165 ASN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8189 moved from start: 0.4907 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= 0.178 Angle : 0.617 7.650 8740 Z= 0.318 Chirality : 0.044 0.139 1021 Planarity : 0.003 0.042 1123 Dihedral : 4.619 20.134 860 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.56 % Allowed : 22.64 % Favored : 76.79 % 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: -0.07 (0.31), residues: 786 helix: 0.35 (1.39), residues: 18 sheet: 0.15 (0.29), residues: 312 loop : -0.12 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 296 HIS 0.003 0.001 HIS B 218 PHE 0.019 0.002 PHE A 172 TYR 0.025 0.001 TYR D 293 ARG 0.009 0.001 ARG B 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 116 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 113 average time/residue: 0.2102 time to fit residues: 31.3894 Evaluate side-chains 106 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0643 time to fit residues: 1.1695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 0.0020 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6414 Z= 0.257 Angle : 0.647 8.060 8740 Z= 0.336 Chirality : 0.044 0.138 1021 Planarity : 0.003 0.035 1123 Dihedral : 4.847 22.676 860 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.56 % Allowed : 23.77 % 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: -0.12 (0.31), residues: 786 helix: 0.24 (1.37), residues: 18 sheet: 0.11 (0.29), residues: 312 loop : -0.14 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 296 HIS 0.002 0.001 HIS D 312 PHE 0.029 0.002 PHE D 247 TYR 0.033 0.002 TYR D 293 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 111 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 108 average time/residue: 0.2015 time to fit residues: 28.2848 Evaluate side-chains 106 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0600 time to fit residues: 1.4323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 16 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.050808 restraints weight = 23078.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.052698 restraints weight = 10939.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054045 restraints weight = 6961.582| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6414 Z= 0.194 Angle : 0.639 7.564 8740 Z= 0.332 Chirality : 0.044 0.141 1021 Planarity : 0.003 0.043 1123 Dihedral : 4.790 23.774 860 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.42 % Allowed : 23.77 % Favored : 75.81 % 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: -0.11 (0.31), residues: 786 helix: 0.41 (1.41), residues: 18 sheet: 0.10 (0.29), residues: 312 loop : -0.13 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 296 HIS 0.003 0.001 HIS B 218 PHE 0.014 0.002 PHE C 182 TYR 0.029 0.001 TYR D 293 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: 1618.02 seconds wall clock time: 30 minutes 55.43 seconds (1855.43 seconds total)