Starting phenix.real_space_refine on Sun Mar 10 14:40:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/03_2024/7vv0_32133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/03_2024/7vv0_32133.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/7vv0_32133/03_2024/7vv0_32133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/03_2024/7vv0_32133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/03_2024/7vv0_32133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/03_2024/7vv0_32133_updated.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 18 5.16 5 C 1477 2.51 5 N 340 2.21 5 O 340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "R GLU 29": "OE1" <-> "OE2" Residue "R ASP 75": "OD1" <-> "OD2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R ARG 143": "NH1" <-> "NH2" Residue "R PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 176": "OD1" <-> "OD2" Residue "R ASP 184": "OD1" <-> "OD2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2175 Number of models: 1 Model: "" Number of chains: 2 Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "R" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2121 Unusual residues: {'CLR': 1} Classifications: {'peptide': 263, 'undetermined': 1} Link IDs: {'PTRANS': 8, 'TRANS': 254, None: 1} Not linked: pdbres="GLN R 288 " pdbres="CLR R 401 " Time building chain proxies: 1.89, per 1000 atoms: 0.87 Number of scatterers: 2175 At special positions: 0 Unit cell: (65.4594, 72.0882, 61.3164, 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 18 16.00 O 340 8.00 N 340 7.00 C 1477 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 474.7 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 502 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'R' and resid 31 through 57 removed outlier: 3.566A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 93 Processing helix chain 'R' and resid 104 through 132 removed outlier: 3.865A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 146 through 159 Processing helix chain 'R' and resid 162 through 168 removed outlier: 4.367A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.992A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 234 Processing helix chain 'R' and resid 237 through 244 Processing helix chain 'R' and resid 246 through 249 No H-bonds generated for 'chain 'R' and resid 246 through 249' Processing helix chain 'R' and resid 257 through 273 Proline residue: R 262 - end of helix Processing helix chain 'R' and resid 275 through 279 146 hydrogen bonds defined for protein. 438 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: 0.52 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 299 1.29 - 1.42: 660 1.42 - 1.55: 1251 1.55 - 1.68: 9 1.68 - 1.81: 22 Bond restraints: 2241 Sorted by residual: bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.426 -0.090 1.36e-02 5.41e+03 4.39e+01 bond pdb=" C LEU R 38 " pdb=" O LEU R 38 " ideal model delta sigma weight residual 1.236 1.157 0.080 1.32e-02 5.74e+03 3.64e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.619 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N TRP R 179 " pdb=" CA TRP R 179 " ideal model delta sigma weight residual 1.458 1.406 0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C TRP R 179 " pdb=" O TRP R 179 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.53e-02 4.27e+03 1.48e+01 ... (remaining 2236 not shown) Histogram of bond angle deviations from ideal: 94.28 - 102.23: 6 102.23 - 110.19: 484 110.19 - 118.15: 1212 118.15 - 126.11: 1295 126.11 - 134.06: 57 Bond angle restraints: 3054 Sorted by residual: angle pdb=" N ARG R 286 " pdb=" CA ARG R 286 " pdb=" C ARG R 286 " ideal model delta sigma weight residual 111.28 123.19 -11.91 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N SER R 284 " pdb=" CA SER R 284 " pdb=" C SER R 284 " ideal model delta sigma weight residual 112.30 122.92 -10.62 1.36e+00 5.41e-01 6.10e+01 angle pdb=" N TRP R 179 " pdb=" CA TRP R 179 " pdb=" C TRP R 179 " ideal model delta sigma weight residual 113.55 104.34 9.21 1.26e+00 6.30e-01 5.34e+01 angle pdb=" N LYS L 11 " pdb=" CA LYS L 11 " pdb=" C LYS L 11 " ideal model delta sigma weight residual 107.93 119.23 -11.30 1.65e+00 3.67e-01 4.69e+01 angle pdb=" C PHE R 285 " pdb=" N ARG R 286 " pdb=" CA ARG R 286 " ideal model delta sigma weight residual 120.28 127.44 -7.16 1.34e+00 5.57e-01 2.85e+01 ... (remaining 3049 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.66: 1071 11.66 - 23.31: 162 23.31 - 34.96: 59 34.96 - 46.61: 20 46.61 - 58.26: 9 Dihedral angle restraints: 1321 sinusoidal: 547 harmonic: 774 Sorted by residual: dihedral pdb=" CB CYS R 26 " pdb=" SG CYS R 26 " pdb=" SG CYS R 258 " pdb=" CB CYS R 258 " ideal model delta sinusoidal sigma weight residual 93.00 151.26 -58.26 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CA GLU R 164 " pdb=" C GLU R 164 " pdb=" N GLY R 165 " pdb=" CA GLY R 165 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C ILE R 32 " pdb=" N ILE R 32 " pdb=" CA ILE R 32 " pdb=" CB ILE R 32 " ideal model delta harmonic sigma weight residual -122.00 -132.39 10.39 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 1318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 342 0.151 - 0.303: 14 0.303 - 0.454: 3 0.454 - 0.605: 1 0.605 - 0.757: 1 Chirality restraints: 361 Sorted by residual: chirality pdb=" CB ILE R 32 " pdb=" CA ILE R 32 " pdb=" CG1 ILE R 32 " pdb=" CG2 ILE R 32 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA SER R 284 " pdb=" N SER R 284 " pdb=" C SER R 284 " pdb=" CB SER R 284 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" CA ARG R 286 " pdb=" N ARG R 286 " pdb=" C ARG R 286 " pdb=" CB ARG R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 358 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 37 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ILE R 37 " 0.069 2.00e-02 2.50e+03 pdb=" O ILE R 37 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU R 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C VAL R 149 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.025 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 151 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C VAL R 151 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL R 151 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU R 152 " -0.021 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 17 2.59 - 3.16: 1683 3.16 - 3.74: 3462 3.74 - 4.32: 4528 4.32 - 4.90: 7434 Nonbonded interactions: 17124 Sorted by model distance: nonbonded pdb=" CD1 LEU R 38 " pdb=" CD1 ILE R 83 " model vdw 2.007 3.880 nonbonded pdb=" O LYS L 12 " pdb=" CE1 PHE R 257 " model vdw 2.215 3.340 nonbonded pdb=" CZ2 TRP L 13 " pdb=" CH2 TRP R 243 " model vdw 2.304 3.640 nonbonded pdb=" NH1 ARG L 10 " pdb=" OD2 ASP R 184 " model vdw 2.311 2.520 nonbonded pdb=" O SER R 284 " pdb=" OG SER R 284 " model vdw 2.317 2.440 ... (remaining 17119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 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: 1.740 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.090 2241 Z= 0.613 Angle : 1.491 15.143 3054 Z= 0.808 Chirality : 0.091 0.757 361 Planarity : 0.012 0.083 354 Dihedral : 14.054 56.619 813 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.93 % Allowed : 1.67 % Favored : 95.40 % Cbeta Deviations : 0.40 % 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: -3.44 (0.39), residues: 264 helix: -2.01 (0.28), residues: 205 sheet: None (None), residues: 0 loop : -2.48 (0.60), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 243 HIS 0.004 0.001 HIS R 261 PHE 0.028 0.003 PHE R 244 TYR 0.012 0.003 TYR R 279 ARG 0.027 0.002 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.240 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.2568 time to fit residues: 8.6867 Evaluate side-chains 26 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2241 Z= 0.210 Angle : 0.662 7.569 3054 Z= 0.323 Chirality : 0.045 0.349 361 Planarity : 0.006 0.046 354 Dihedral : 9.500 58.463 366 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.93 % Allowed : 9.21 % Favored : 87.87 % 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: -0.39 (0.49), residues: 264 helix: 0.28 (0.34), residues: 210 sheet: None (None), residues: 0 loop : -2.11 (0.73), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 154 HIS 0.001 0.000 HIS R 144 PHE 0.014 0.001 PHE R 244 TYR 0.004 0.001 TYR R 113 ARG 0.004 0.001 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.249 Fit side-chains REVERT: R 45 LEU cc_start: 0.8568 (mm) cc_final: 0.8348 (mm) REVERT: R 287 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6459 (tmtt) outliers start: 7 outliers final: 4 residues processed: 34 average time/residue: 0.2030 time to fit residues: 7.9757 Evaluate side-chains 30 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.0030 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2241 Z= 0.176 Angle : 0.589 6.198 3054 Z= 0.283 Chirality : 0.043 0.319 361 Planarity : 0.004 0.039 354 Dihedral : 7.999 58.980 356 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.18 % Allowed : 12.13 % Favored : 83.68 % 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: 0.97 (0.52), residues: 264 helix: 1.27 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.77 (0.76), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 13 HIS 0.000 0.000 HIS R 261 PHE 0.010 0.001 PHE R 244 TYR 0.006 0.001 TYR R 113 ARG 0.004 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 26 time to evaluate : 0.241 Fit side-chains REVERT: R 45 LEU cc_start: 0.8477 (mm) cc_final: 0.8236 (mm) REVERT: R 287 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6446 (tmtt) outliers start: 10 outliers final: 6 residues processed: 32 average time/residue: 0.1768 time to fit residues: 6.6720 Evaluate side-chains 33 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0070 chunk 24 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2241 Z= 0.130 Angle : 0.518 5.421 3054 Z= 0.250 Chirality : 0.038 0.289 361 Planarity : 0.004 0.036 354 Dihedral : 7.272 55.663 356 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.18 % Allowed : 13.81 % Favored : 82.01 % 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: 1.75 (0.53), residues: 264 helix: 1.83 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -1.49 (0.77), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 133 HIS 0.001 0.000 HIS R 259 PHE 0.016 0.001 PHE R 257 TYR 0.007 0.001 TYR R 113 ARG 0.005 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.241 Fit side-chains REVERT: R 45 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8072 (mm) REVERT: R 285 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: R 287 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6308 (tmtt) outliers start: 10 outliers final: 6 residues processed: 29 average time/residue: 0.2129 time to fit residues: 7.0875 Evaluate side-chains 30 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 21 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2241 Z= 0.173 Angle : 0.550 5.477 3054 Z= 0.266 Chirality : 0.040 0.288 361 Planarity : 0.004 0.031 354 Dihedral : 7.242 55.843 356 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.44 % Allowed : 14.64 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.89 (0.53), residues: 264 helix: 1.90 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -1.28 (0.78), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 154 HIS 0.000 0.000 HIS R 259 PHE 0.011 0.001 PHE R 257 TYR 0.010 0.001 TYR R 279 ARG 0.006 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 28 time to evaluate : 0.244 Fit side-chains REVERT: R 45 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8064 (mm) REVERT: R 285 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6402 (m-80) REVERT: R 287 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.6322 (tmtt) outliers start: 13 outliers final: 9 residues processed: 34 average time/residue: 0.1977 time to fit residues: 7.7688 Evaluate side-chains 39 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 27 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2241 Z= 0.153 Angle : 0.534 5.387 3054 Z= 0.257 Chirality : 0.039 0.267 361 Planarity : 0.004 0.030 354 Dihedral : 7.313 59.363 356 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.44 % Allowed : 15.48 % Favored : 79.08 % 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: 2.06 (0.53), residues: 264 helix: 2.03 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -1.28 (0.77), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 243 HIS 0.000 0.000 HIS R 144 PHE 0.017 0.001 PHE R 257 TYR 0.007 0.001 TYR R 113 ARG 0.005 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 20 time to evaluate : 0.259 Fit side-chains REVERT: R 45 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8064 (mm) REVERT: R 285 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.6325 (m-80) REVERT: R 287 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6410 (tmtt) outliers start: 13 outliers final: 9 residues processed: 27 average time/residue: 0.1845 time to fit residues: 5.8739 Evaluate side-chains 32 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 20 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.0170 chunk 24 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2241 Z= 0.166 Angle : 0.538 5.493 3054 Z= 0.260 Chirality : 0.039 0.261 361 Planarity : 0.004 0.030 354 Dihedral : 7.270 59.859 356 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.44 % Allowed : 16.74 % Favored : 77.82 % 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: 2.05 (0.53), residues: 264 helix: 2.01 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.29 (0.80), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 243 HIS 0.001 0.000 HIS R 259 PHE 0.015 0.001 PHE R 257 TYR 0.007 0.001 TYR R 113 ARG 0.005 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 26 time to evaluate : 0.239 Fit side-chains REVERT: R 45 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8023 (mm) REVERT: R 285 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.6295 (m-80) REVERT: R 287 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.6341 (tmtt) outliers start: 13 outliers final: 9 residues processed: 33 average time/residue: 0.1694 time to fit residues: 6.5736 Evaluate side-chains 37 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.0570 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2241 Z= 0.152 Angle : 0.524 5.406 3054 Z= 0.255 Chirality : 0.038 0.240 361 Planarity : 0.004 0.029 354 Dihedral : 7.080 56.763 356 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.44 % Allowed : 17.15 % Favored : 77.41 % 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: 2.15 (0.53), residues: 264 helix: 2.09 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.30 (0.81), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 190 HIS 0.000 0.000 HIS R 259 PHE 0.014 0.001 PHE R 257 TYR 0.007 0.001 TYR R 113 ARG 0.006 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 21 time to evaluate : 0.224 Fit side-chains REVERT: R 45 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8000 (mm) REVERT: R 285 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.6301 (m-80) REVERT: R 287 LYS cc_start: 0.6564 (OUTLIER) cc_final: 0.6351 (tmtt) outliers start: 13 outliers final: 9 residues processed: 28 average time/residue: 0.1827 time to fit residues: 5.9948 Evaluate side-chains 33 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 21 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2241 Z= 0.164 Angle : 0.532 5.434 3054 Z= 0.259 Chirality : 0.039 0.236 361 Planarity : 0.004 0.030 354 Dihedral : 7.063 56.093 356 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.44 % Allowed : 17.99 % Favored : 76.57 % 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: 2.12 (0.53), residues: 264 helix: 2.05 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.29 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 190 HIS 0.000 0.000 HIS R 259 PHE 0.014 0.001 PHE R 257 TYR 0.007 0.001 TYR R 113 ARG 0.006 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 26 time to evaluate : 0.257 Fit side-chains REVERT: R 45 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8013 (mm) REVERT: R 285 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.6314 (m-80) outliers start: 13 outliers final: 9 residues processed: 33 average time/residue: 0.1745 time to fit residues: 6.7767 Evaluate side-chains 37 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2241 Z= 0.171 Angle : 0.537 5.432 3054 Z= 0.261 Chirality : 0.039 0.229 361 Planarity : 0.004 0.031 354 Dihedral : 6.767 54.626 352 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.60 % Allowed : 18.83 % Favored : 76.57 % 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: 2.10 (0.53), residues: 264 helix: 2.04 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.29 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 190 HIS 0.000 0.000 HIS R 259 PHE 0.020 0.001 PHE R 93 TYR 0.007 0.001 TYR R 113 ARG 0.006 0.000 ARG R 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 0.242 Fit side-chains REVERT: R 45 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8006 (mm) REVERT: R 285 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6345 (m-80) outliers start: 11 outliers final: 9 residues processed: 32 average time/residue: 0.1563 time to fit residues: 5.9892 Evaluate side-chains 37 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 103 SER Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.155564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126733 restraints weight = 2235.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130632 restraints weight = 1260.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133135 restraints weight = 901.836| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2241 Z= 0.189 Angle : 0.552 5.529 3054 Z= 0.270 Chirality : 0.040 0.233 361 Planarity : 0.004 0.032 354 Dihedral : 6.837 55.099 352 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.60 % Allowed : 18.83 % Favored : 76.57 % 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: 2.02 (0.53), residues: 264 helix: 1.99 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.36 (0.81), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 190 HIS 0.001 0.000 HIS R 259 PHE 0.021 0.001 PHE R 257 TYR 0.007 0.001 TYR R 113 ARG 0.006 0.000 ARG R 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1021.23 seconds wall clock time: 19 minutes 1.58 seconds (1141.58 seconds total)