Starting phenix.real_space_refine on Tue Feb 13 10:10:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2024/7yi9_33854_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2024/7yi9_33854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2024/7yi9_33854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2024/7yi9_33854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2024/7yi9_33854_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2024/7yi9_33854_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.076 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 27 5.16 5 C 3335 2.51 5 N 892 2.21 5 O 972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 162": "OE1" <-> "OE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D GLU 115": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5226 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2117 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1819 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 269 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 994 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 3.35, per 1000 atoms: 0.64 Number of scatterers: 5226 At special positions: 0 Unit cell: (80.75, 68, 122.4, 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 27 16.00 O 972 8.00 N 892 7.00 C 3335 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: 2.05 Conformation dependent library (CDL) restraints added in 901.4 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 2 sheets defined 33.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 166 through 169 Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.590A pdb=" N LYS A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 321 through 333 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'B' and resid 141 through 166 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 240 through 243 No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 255 through 267 removed outlier: 5.318A pdb=" N ARG B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.537A pdb=" N GLU C 157 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN C 158 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 158' Processing helix chain 'C' and resid 170 through 182 removed outlier: 4.420A pdb=" N ALA C 175 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 25 Processing helix chain 'D' and resid 39 through 42 No H-bonds generated for 'chain 'D' and resid 39 through 42' Processing helix chain 'D' and resid 52 through 65 Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 84 through 95 removed outlier: 4.639A pdb=" N CYS D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 114 through 117 No H-bonds generated for 'chain 'D' and resid 114 through 117' Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing sheet with id= A, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.227A pdb=" N ALA A 146 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU A 432 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 148 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 183 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE A 149 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE A 185 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 182 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR A 361 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 364 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 209 " --> pdb=" O MET A 364 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG A 366 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR A 207 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 177 through 180 removed outlier: 6.520A pdb=" N TYR B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE B 368 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU B 353 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 205 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE B 354 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET B 207 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE B 248 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N MET B 208 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE B 250 " --> pdb=" O MET B 208 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 301 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 306 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU B 272 " --> pdb=" O VAL B 306 " (cutoff:3.500A) 148 hydrogen bonds defined for protein. 387 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: 1.19 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1686 1.34 - 1.46: 761 1.46 - 1.57: 2824 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5319 Sorted by residual: bond pdb=" C2 SAM B 401 " pdb=" N3 SAM B 401 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" C8 SAM B 401 " pdb=" N7 SAM B 401 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.10e+00 bond pdb=" C2 SAM B 401 " pdb=" N1 SAM B 401 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C6 SAM B 401 " pdb=" N1 SAM B 401 " ideal model delta sigma weight residual 1.337 1.377 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C1' SAM B 401 " pdb=" N9 SAM B 401 " ideal model delta sigma weight residual 1.452 1.478 -0.026 2.00e-02 2.50e+03 1.67e+00 ... (remaining 5314 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.13: 86 106.13 - 113.11: 2875 113.11 - 120.08: 1863 120.08 - 127.06: 2280 127.06 - 134.04: 45 Bond angle restraints: 7149 Sorted by residual: angle pdb=" N ILE A 337 " pdb=" CA ILE A 337 " pdb=" C ILE A 337 " ideal model delta sigma weight residual 111.90 107.94 3.96 8.10e-01 1.52e+00 2.38e+01 angle pdb=" C LEU D 87 " pdb=" N GLU D 88 " pdb=" CA GLU D 88 " ideal model delta sigma weight residual 122.38 115.48 6.90 1.81e+00 3.05e-01 1.45e+01 angle pdb=" CA GLU D 88 " pdb=" CB GLU D 88 " pdb=" CG GLU D 88 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.30e+00 angle pdb=" O SAM B 401 " pdb=" C SAM B 401 " pdb=" OXT SAM B 401 " ideal model delta sigma weight residual 126.77 117.87 8.90 3.00e+00 1.11e-01 8.79e+00 angle pdb=" N1 SAM B 401 " pdb=" C2 SAM B 401 " pdb=" N3 SAM B 401 " ideal model delta sigma weight residual 128.51 120.01 8.50 3.00e+00 1.11e-01 8.02e+00 ... (remaining 7144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 2898 17.48 - 34.95: 294 34.95 - 52.43: 61 52.43 - 69.90: 7 69.90 - 87.38: 8 Dihedral angle restraints: 3268 sinusoidal: 1413 harmonic: 1855 Sorted by residual: dihedral pdb=" CA LEU A 178 " pdb=" C LEU A 178 " pdb=" N MET A 179 " pdb=" CA MET A 179 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA MET A 402 " pdb=" C MET A 402 " pdb=" N LYS A 403 " pdb=" CA LYS A 403 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA HIS A 379 " pdb=" C HIS A 379 " pdb=" N GLN A 380 " pdb=" CA GLN A 380 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.218: 780 2.218 - 4.436: 0 4.436 - 6.654: 0 6.654 - 8.872: 0 8.872 - 11.090: 1 Chirality restraints: 781 Sorted by residual: chirality pdb=" SD SAM B 401 " pdb=" CG SAM B 401 " pdb=" CE SAM B 401 " pdb=" C5' SAM B 401 " both_signs ideal model delta sigma weight residual False 5.50 -5.59 11.09 2.00e-01 2.50e+01 3.07e+03 chirality pdb=" CA GLN B 161 " pdb=" N GLN B 161 " pdb=" C GLN B 161 " pdb=" CB GLN B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" C2' SAM B 401 " pdb=" C1' SAM B 401 " pdb=" C3' SAM B 401 " pdb=" O2' SAM B 401 " both_signs ideal model delta sigma weight residual False -2.76 -2.59 -0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 778 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 112 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO A 113 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 352 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO A 353 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 174 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 175 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " -0.020 5.00e-02 4.00e+02 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 69 2.67 - 3.23: 4872 3.23 - 3.79: 7747 3.79 - 4.34: 11272 4.34 - 4.90: 17994 Nonbonded interactions: 41954 Sorted by model distance: nonbonded pdb=" O LEU C 164 " pdb=" OH TYR C 171 " model vdw 2.115 2.440 nonbonded pdb=" NE2 GLN A 380 " pdb=" O GLY B 292 " model vdw 2.193 2.520 nonbonded pdb=" OD1 ASN A 210 " pdb=" OG1 THR A 361 " model vdw 2.237 2.440 nonbonded pdb=" NE1 TRP A 153 " pdb=" O TRP A 187 " model vdw 2.255 2.520 nonbonded pdb=" OD2 ASP B 204 " pdb=" NH1 ARG B 314 " model vdw 2.260 2.520 ... (remaining 41949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 3.220 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.180 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 : 0.004 0.056 5319 Z= 0.229 Angle : 0.651 8.895 7149 Z= 0.340 Chirality : 0.399 11.090 781 Planarity : 0.004 0.054 909 Dihedral : 14.607 87.381 2062 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.33), residues: 620 helix: -0.03 (0.36), residues: 204 sheet: 0.53 (0.52), residues: 102 loop : -1.23 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 50 HIS 0.002 0.001 HIS C 169 PHE 0.014 0.002 PHE B 158 TYR 0.008 0.001 TYR B 258 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.698 Fit side-chains REVERT: B 371 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7381 (pp20) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 1.3075 time to fit residues: 137.3028 Evaluate side-chains 79 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 0.0980 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 334 ASN B 213 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5319 Z= 0.177 Angle : 0.547 5.959 7149 Z= 0.292 Chirality : 0.041 0.136 781 Planarity : 0.004 0.052 909 Dihedral : 6.966 56.502 707 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.25 % Allowed : 12.13 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.33), residues: 620 helix: 0.21 (0.37), residues: 203 sheet: 0.62 (0.50), residues: 102 loop : -1.25 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 212 HIS 0.002 0.001 HIS B 291 PHE 0.017 0.002 PHE A 419 TYR 0.009 0.001 TYR A 207 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.638 Fit side-chains REVERT: A 223 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6697 (mt0) REVERT: A 381 ARG cc_start: 0.7738 (mmm-85) cc_final: 0.7340 (mmt-90) REVERT: B 371 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7386 (pp20) REVERT: B 372 LEU cc_start: 0.7179 (tt) cc_final: 0.6831 (tp) REVERT: D 27 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.7125 (m110) REVERT: D 110 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6149 (mp0) REVERT: D 114 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.4910 (tt0) outliers start: 13 outliers final: 5 residues processed: 83 average time/residue: 1.3120 time to fit residues: 113.3590 Evaluate side-chains 83 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 38 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5319 Z= 0.203 Angle : 0.535 5.247 7149 Z= 0.288 Chirality : 0.041 0.139 781 Planarity : 0.004 0.053 909 Dihedral : 6.652 59.423 707 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.77 % Allowed : 14.90 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.33), residues: 620 helix: 0.08 (0.37), residues: 203 sheet: 0.67 (0.50), residues: 102 loop : -1.26 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 212 HIS 0.002 0.001 HIS B 291 PHE 0.014 0.002 PHE B 158 TYR 0.006 0.001 TYR A 407 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.607 Fit side-chains REVERT: A 223 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6709 (mt0) REVERT: A 326 GLN cc_start: 0.6390 (OUTLIER) cc_final: 0.5953 (pt0) REVERT: A 431 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 289 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7776 (mppt) REVERT: D 63 GLU cc_start: 0.6269 (pp20) cc_final: 0.5904 (tm-30) REVERT: D 114 GLU cc_start: 0.5537 (OUTLIER) cc_final: 0.4953 (tt0) outliers start: 16 outliers final: 7 residues processed: 85 average time/residue: 1.3389 time to fit residues: 118.3567 Evaluate side-chains 81 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 360 HIS A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5319 Z= 0.300 Angle : 0.601 5.829 7149 Z= 0.323 Chirality : 0.043 0.155 781 Planarity : 0.005 0.055 909 Dihedral : 6.666 56.122 707 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.68 % Allowed : 15.25 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.33), residues: 620 helix: -0.17 (0.36), residues: 203 sheet: 0.49 (0.50), residues: 103 loop : -1.39 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 212 HIS 0.002 0.001 HIS B 291 PHE 0.012 0.002 PHE B 250 TYR 0.012 0.002 TYR B 153 ARG 0.004 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 0.618 Fit side-chains REVERT: A 223 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6698 (mt0) REVERT: A 326 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.5970 (pt0) REVERT: A 376 GLU cc_start: 0.5996 (tm-30) cc_final: 0.5776 (tm-30) REVERT: A 429 MET cc_start: 0.8099 (mtt) cc_final: 0.7729 (mtt) REVERT: B 372 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7194 (tp) REVERT: D 110 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5907 (mp0) REVERT: D 114 GLU cc_start: 0.5488 (OUTLIER) cc_final: 0.5008 (tt0) outliers start: 27 outliers final: 14 residues processed: 89 average time/residue: 1.3319 time to fit residues: 123.1405 Evaluate side-chains 90 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0170 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 0.0040 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.4630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5319 Z= 0.141 Angle : 0.486 5.047 7149 Z= 0.264 Chirality : 0.039 0.133 781 Planarity : 0.004 0.053 909 Dihedral : 6.039 45.283 707 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.47 % Allowed : 18.20 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.33), residues: 620 helix: 0.28 (0.37), residues: 196 sheet: 0.67 (0.52), residues: 98 loop : -1.14 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 212 HIS 0.002 0.001 HIS B 291 PHE 0.014 0.001 PHE B 158 TYR 0.011 0.001 TYR B 153 ARG 0.003 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.668 Fit side-chains REVERT: A 381 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7458 (mmt-90) REVERT: B 289 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7552 (mppt) REVERT: B 371 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7444 (pp20) REVERT: B 372 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.6996 (tp) REVERT: D 110 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.6002 (mp0) REVERT: D 114 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.4888 (tt0) outliers start: 20 outliers final: 8 residues processed: 81 average time/residue: 1.4189 time to fit residues: 119.6644 Evaluate side-chains 83 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 4 optimal weight: 0.0570 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 0.0050 chunk 34 optimal weight: 0.9990 overall best weight: 0.6716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5319 Z= 0.156 Angle : 0.496 6.189 7149 Z= 0.267 Chirality : 0.040 0.136 781 Planarity : 0.004 0.053 909 Dihedral : 5.929 44.260 707 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.64 % Allowed : 18.02 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.33), residues: 620 helix: 0.34 (0.38), residues: 196 sheet: 0.67 (0.52), residues: 98 loop : -1.11 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 212 HIS 0.003 0.001 HIS B 291 PHE 0.010 0.001 PHE B 158 TYR 0.008 0.001 TYR B 153 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.642 Fit side-chains REVERT: A 223 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.7028 (mm-40) REVERT: A 381 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7488 (mmt90) REVERT: B 289 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7614 (mppt) REVERT: B 371 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7445 (pp20) REVERT: B 372 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7028 (tp) REVERT: D 110 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5823 (mp0) REVERT: D 114 GLU cc_start: 0.5445 (OUTLIER) cc_final: 0.4874 (tt0) outliers start: 21 outliers final: 9 residues processed: 84 average time/residue: 1.4382 time to fit residues: 125.6714 Evaluate side-chains 87 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5319 Z= 0.362 Angle : 0.665 8.363 7149 Z= 0.352 Chirality : 0.045 0.175 781 Planarity : 0.005 0.055 909 Dihedral : 6.614 47.071 707 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.99 % Allowed : 18.72 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.33), residues: 620 helix: -0.11 (0.36), residues: 199 sheet: 0.32 (0.53), residues: 93 loop : -1.39 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 212 HIS 0.003 0.001 HIS B 291 PHE 0.013 0.002 PHE D 14 TYR 0.011 0.002 TYR A 207 ARG 0.004 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 68 time to evaluate : 0.615 Fit side-chains REVERT: A 223 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6820 (mt0) REVERT: A 381 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7560 (mmt-90) REVERT: B 171 MET cc_start: 0.5290 (pmm) cc_final: 0.4597 (pp-130) REVERT: B 371 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7450 (pp20) REVERT: B 372 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7170 (tp) REVERT: D 88 GLU cc_start: 0.6262 (pm20) cc_final: 0.5942 (pm20) REVERT: D 110 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5774 (mp0) REVERT: D 114 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.5119 (tt0) outliers start: 23 outliers final: 9 residues processed: 83 average time/residue: 1.3265 time to fit residues: 114.5814 Evaluate side-chains 79 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN B 155 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5319 Z= 0.169 Angle : 0.538 7.639 7149 Z= 0.287 Chirality : 0.040 0.163 781 Planarity : 0.004 0.052 909 Dihedral : 6.002 44.048 707 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.99 % Allowed : 19.24 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.33), residues: 620 helix: 0.18 (0.37), residues: 197 sheet: 0.61 (0.50), residues: 103 loop : -1.11 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 212 HIS 0.003 0.001 HIS B 291 PHE 0.011 0.001 PHE B 158 TYR 0.006 0.001 TYR B 153 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 0.627 Fit side-chains REVERT: A 223 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6796 (mt0) REVERT: B 371 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7385 (pp20) REVERT: B 372 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7089 (tp) REVERT: D 88 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.6056 (pm20) REVERT: D 110 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5801 (mp0) REVERT: D 114 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.4976 (tt0) outliers start: 23 outliers final: 8 residues processed: 82 average time/residue: 1.2521 time to fit residues: 107.0964 Evaluate side-chains 79 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5319 Z= 0.234 Angle : 0.582 9.939 7149 Z= 0.307 Chirality : 0.042 0.167 781 Planarity : 0.004 0.053 909 Dihedral : 6.086 44.052 707 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.12 % Allowed : 20.28 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.34), residues: 620 helix: 0.14 (0.37), residues: 197 sheet: 0.56 (0.50), residues: 103 loop : -1.13 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 212 HIS 0.004 0.001 HIS B 291 PHE 0.012 0.001 PHE B 250 TYR 0.009 0.001 TYR A 207 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.706 Fit side-chains REVERT: A 223 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6785 (mt0) REVERT: B 171 MET cc_start: 0.5247 (pmm) cc_final: 0.4562 (pp-130) REVERT: B 372 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7152 (tp) REVERT: D 88 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.6053 (pm20) REVERT: D 110 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5728 (mp0) REVERT: D 114 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.4992 (tt0) outliers start: 18 outliers final: 10 residues processed: 75 average time/residue: 1.3659 time to fit residues: 107.2907 Evaluate side-chains 82 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 161 GLN B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5319 Z= 0.255 Angle : 0.605 9.367 7149 Z= 0.320 Chirality : 0.042 0.158 781 Planarity : 0.004 0.054 909 Dihedral : 6.128 43.720 707 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.47 % Allowed : 20.80 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.33), residues: 620 helix: 0.10 (0.37), residues: 197 sheet: 0.47 (0.50), residues: 104 loop : -1.20 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 212 HIS 0.004 0.001 HIS B 291 PHE 0.012 0.002 PHE B 250 TYR 0.007 0.001 TYR B 339 ARG 0.005 0.001 ARG A 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 0.611 Fit side-chains REVERT: A 223 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6819 (mt0) REVERT: B 171 MET cc_start: 0.5263 (pmm) cc_final: 0.4532 (pp-130) REVERT: B 207 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7617 (ttp) REVERT: B 371 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7346 (pp20) REVERT: B 372 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7183 (tp) REVERT: D 88 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6107 (pm20) REVERT: D 110 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5711 (mp0) REVERT: D 114 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.5029 (tt0) outliers start: 20 outliers final: 12 residues processed: 78 average time/residue: 1.3127 time to fit residues: 106.7001 Evaluate side-chains 78 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.193738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145828 restraints weight = 5935.836| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.32 r_work: 0.3776 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5319 Z= 0.158 Angle : 0.530 8.809 7149 Z= 0.282 Chirality : 0.040 0.134 781 Planarity : 0.004 0.052 909 Dihedral : 5.789 43.931 707 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.29 % Allowed : 20.97 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.34), residues: 620 helix: 0.35 (0.37), residues: 195 sheet: 0.68 (0.51), residues: 102 loop : -1.10 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 212 HIS 0.003 0.001 HIS B 291 PHE 0.009 0.001 PHE B 250 TYR 0.005 0.001 TYR B 270 ARG 0.002 0.000 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2576.77 seconds wall clock time: 46 minutes 26.82 seconds (2786.82 seconds total)