Starting phenix.real_space_refine on Sun Mar 10 14:46:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/03_2024/7vv6_32139_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/03_2024/7vv6_32139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/03_2024/7vv6_32139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/03_2024/7vv6_32139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/03_2024/7vv6_32139_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/03_2024/7vv6_32139_updated.pdb" } resolution = 3.3 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 1518 2.51 5 N 342 2.21 5 O 349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 141": "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 PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 254": "OD1" <-> "OD2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 285": "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: 2227 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2227 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'peptide': 271, 'undetermined': 2} Link IDs: {'PTRANS': 8, 'TRANS': 262, None: 2} Not linked: pdbres="TRP R 289 " pdbres="CLR R 401 " Not linked: pdbres="CLR R 401 " pdbres="6IB R 402 " Time building chain proxies: 1.91, per 1000 atoms: 0.86 Number of scatterers: 2227 At special positions: 0 Unit cell: (65.224, 72.588, 61.016, 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 349 8.00 N 342 7.00 C 1518 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=2.04 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: 0.91 Conformation dependent library (CDL) restraints added in 402.1 milliseconds 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'R' and resid 31 through 56 Processing helix chain 'R' and resid 63 through 93 removed outlier: 4.251A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 132 Processing helix chain 'R' and resid 134 through 138 Processing helix chain 'R' and resid 145 through 167 Processing helix chain 'R' and resid 177 through 211 removed outlier: 3.926A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 235 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 279 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 281 through 287 removed outlier: 4.497A pdb=" N ARG R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS R 287 " --> pdb=" O GLY R 283 " (cutoff:3.500A) 152 hydrogen bonds defined for protein. 456 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: 0.67 Time building geometry restraints manager: 0.99 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: 617 1.34 - 1.47: 662 1.47 - 1.59: 993 1.59 - 1.71: 1 1.71 - 1.84: 22 Bond restraints: 2295 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.669 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.99e+00 bond pdb=" C31 6IB R 402 " pdb=" N5 6IB R 402 " ideal model delta sigma weight residual 1.447 1.496 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C32 6IB R 402 " pdb=" N6 6IB R 402 " ideal model delta sigma weight residual 1.449 1.497 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" CB VAL R 131 " pdb=" CG2 VAL R 131 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 ... (remaining 2290 not shown) Histogram of bond angle deviations from ideal: 96.18 - 103.83: 25 103.83 - 111.48: 903 111.48 - 119.13: 970 119.13 - 126.77: 1187 126.77 - 134.42: 46 Bond angle restraints: 3131 Sorted by residual: angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 113.45 120.88 -7.43 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C TRP R 250 " pdb=" N LYS R 251 " pdb=" CA LYS R 251 " ideal model delta sigma weight residual 122.08 129.29 -7.21 1.47e+00 4.63e-01 2.41e+01 angle pdb=" C GLY R 236 " pdb=" N LEU R 237 " pdb=" CA LEU R 237 " ideal model delta sigma weight residual 120.58 127.01 -6.43 1.32e+00 5.74e-01 2.37e+01 angle pdb=" CA LEU R 226 " pdb=" CB LEU R 226 " pdb=" CG LEU R 226 " ideal model delta sigma weight residual 116.30 132.37 -16.07 3.50e+00 8.16e-02 2.11e+01 angle pdb=" N SER R 177 " pdb=" CA SER R 177 " pdb=" C SER R 177 " ideal model delta sigma weight residual 111.28 115.95 -4.67 1.09e+00 8.42e-01 1.83e+01 ... (remaining 3126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.72: 1034 12.72 - 25.44: 169 25.44 - 38.16: 97 38.16 - 50.88: 34 50.88 - 63.60: 21 Dihedral angle restraints: 1355 sinusoidal: 571 harmonic: 784 Sorted by residual: dihedral pdb=" CA THR R 30 " pdb=" C THR R 30 " pdb=" N LEU R 31 " pdb=" CA LEU R 31 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP R 254 " pdb=" C ASP R 254 " pdb=" N VAL R 255 " pdb=" CA VAL R 255 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASP R 252 " pdb=" C ASP R 252 " pdb=" N SER R 253 " pdb=" CA SER R 253 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 1352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 253 0.061 - 0.122: 88 0.122 - 0.183: 23 0.183 - 0.244: 2 0.244 - 0.305: 2 Chirality restraints: 368 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C9 CLR R 401 " pdb=" C10 CLR R 401 " pdb=" C11 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 365 not shown) Planarity restraints: 361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL R 149 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 43 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C VAL R 43 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL R 43 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY R 44 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 40 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ILE R 40 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 40 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA R 41 " -0.013 2.00e-02 2.50e+03 ... (remaining 358 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 629 2.81 - 3.33: 1957 3.33 - 3.86: 3872 3.86 - 4.38: 4203 4.38 - 4.90: 7429 Nonbonded interactions: 18090 Sorted by model distance: nonbonded pdb=" O GLY R 27 " pdb=" OH TYR R 89 " model vdw 2.291 2.440 nonbonded pdb=" O SER R 264 " pdb=" OG SER R 268 " model vdw 2.306 2.440 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.320 2.440 nonbonded pdb=" O SER R 98 " pdb=" OG SER R 98 " model vdw 2.322 2.440 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.322 2.440 ... (remaining 18085 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.940 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.890 Find NCS groups from input model: 0.050 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 0.134 2295 Z= 0.587 Angle : 1.380 16.073 3131 Z= 0.707 Chirality : 0.068 0.305 368 Planarity : 0.009 0.048 361 Dihedral : 19.052 63.599 841 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 10.37 % Allowed : 24.90 % Favored : 64.73 % 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: -4.22 (0.34), residues: 269 helix: -2.49 (0.23), residues: 208 sheet: None (None), residues: 0 loop : -3.08 (0.63), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP R 289 HIS 0.004 0.001 HIS R 261 PHE 0.020 0.003 PHE R 183 TYR 0.021 0.004 TYR R 89 ARG 0.005 0.001 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: R 109 MET cc_start: 0.8310 (ttp) cc_final: 0.7998 (ttm) REVERT: R 164 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7868 (tm-30) REVERT: R 166 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8433 (tptt) REVERT: R 201 SER cc_start: 0.9194 (m) cc_final: 0.8684 (p) REVERT: R 242 GLN cc_start: 0.8817 (pp30) cc_final: 0.8517 (pp30) outliers start: 25 outliers final: 1 residues processed: 67 average time/residue: 0.1199 time to fit residues: 9.6167 Evaluate side-chains 31 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2295 Z= 0.170 Angle : 0.621 9.267 3131 Z= 0.295 Chirality : 0.042 0.221 368 Planarity : 0.005 0.034 361 Dihedral : 10.744 59.124 380 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.15 % Allowed : 26.97 % Favored : 68.88 % 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: -0.05 (0.48), residues: 269 helix: 0.62 (0.33), residues: 211 sheet: None (None), residues: 0 loop : -2.28 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 248 HIS 0.002 0.001 HIS R 144 PHE 0.010 0.001 PHE R 183 TYR 0.009 0.001 TYR R 222 ARG 0.006 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.245 Fit side-chains REVERT: R 59 MET cc_start: 0.8233 (mtt) cc_final: 0.7879 (mtt) REVERT: R 166 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8271 (tptt) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.1237 time to fit residues: 6.6751 Evaluate side-chains 39 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 246 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2295 Z= 0.239 Angle : 0.591 6.743 3131 Z= 0.287 Chirality : 0.042 0.176 368 Planarity : 0.004 0.033 361 Dihedral : 9.744 58.186 380 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.73 % Allowed : 25.31 % Favored : 70.95 % 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: 1.59 (0.52), residues: 269 helix: 1.84 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.98 (0.80), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 243 HIS 0.001 0.001 HIS R 259 PHE 0.010 0.001 PHE R 183 TYR 0.012 0.002 TYR R 222 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.248 Fit side-chains REVERT: R 166 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8347 (tptt) REVERT: R 181 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: R 242 GLN cc_start: 0.8892 (pp30) cc_final: 0.8577 (pp30) outliers start: 9 outliers final: 7 residues processed: 41 average time/residue: 0.1279 time to fit residues: 6.3739 Evaluate side-chains 39 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2295 Z= 0.172 Angle : 0.526 6.077 3131 Z= 0.257 Chirality : 0.040 0.153 368 Planarity : 0.003 0.031 361 Dihedral : 9.009 55.459 380 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.98 % Allowed : 25.73 % Favored : 69.29 % 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: 2.18 (0.53), residues: 269 helix: 2.27 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.87 (0.82), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.007 0.001 PHE R 183 TYR 0.015 0.002 TYR R 222 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.253 Fit side-chains REVERT: R 38 LEU cc_start: 0.8840 (tp) cc_final: 0.8533 (tp) REVERT: R 75 ASP cc_start: 0.8525 (m-30) cc_final: 0.8156 (t0) REVERT: R 163 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8466 (tt) REVERT: R 166 LYS cc_start: 0.8993 (ttpp) cc_final: 0.8360 (tptt) REVERT: R 242 GLN cc_start: 0.8911 (pp30) cc_final: 0.8461 (pp30) outliers start: 12 outliers final: 10 residues processed: 48 average time/residue: 0.1156 time to fit residues: 6.8177 Evaluate side-chains 44 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2295 Z= 0.153 Angle : 0.509 5.971 3131 Z= 0.246 Chirality : 0.039 0.156 368 Planarity : 0.003 0.031 361 Dihedral : 8.763 59.690 380 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.15 % Allowed : 26.14 % Favored : 69.71 % 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: 2.55 (0.53), residues: 269 helix: 2.52 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.71 (0.82), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 183 TYR 0.012 0.002 TYR R 222 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.253 Fit side-chains REVERT: R 38 LEU cc_start: 0.8855 (tp) cc_final: 0.8554 (tp) REVERT: R 163 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8462 (tt) REVERT: R 166 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8375 (tptt) outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.1136 time to fit residues: 6.5268 Evaluate side-chains 45 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2295 Z= 0.163 Angle : 0.502 6.034 3131 Z= 0.244 Chirality : 0.039 0.157 368 Planarity : 0.003 0.030 361 Dihedral : 8.659 57.253 380 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.98 % Allowed : 26.97 % Favored : 68.05 % 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: 2.75 (0.53), residues: 269 helix: 2.65 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.61 (0.83), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 64 TYR 0.010 0.001 TYR R 279 ARG 0.001 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 0.274 Fit side-chains REVERT: R 38 LEU cc_start: 0.8858 (tp) cc_final: 0.8546 (tp) REVERT: R 75 ASP cc_start: 0.8555 (m-30) cc_final: 0.8220 (t0) REVERT: R 166 LYS cc_start: 0.9021 (ttpp) cc_final: 0.8377 (tptt) REVERT: R 181 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8228 (tt0) outliers start: 12 outliers final: 10 residues processed: 46 average time/residue: 0.1172 time to fit residues: 6.6102 Evaluate side-chains 44 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2295 Z= 0.157 Angle : 0.502 5.994 3131 Z= 0.243 Chirality : 0.039 0.159 368 Planarity : 0.003 0.030 361 Dihedral : 8.347 53.500 380 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.56 % Allowed : 28.22 % Favored : 67.22 % 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: 2.89 (0.53), residues: 269 helix: 2.74 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.50 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.007 0.001 PHE R 64 TYR 0.010 0.001 TYR R 279 ARG 0.001 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.254 Fit side-chains REVERT: R 38 LEU cc_start: 0.8859 (tp) cc_final: 0.8562 (tp) REVERT: R 75 ASP cc_start: 0.8558 (m-30) cc_final: 0.8221 (t0) REVERT: R 166 LYS cc_start: 0.9070 (ttpp) cc_final: 0.8675 (tptt) REVERT: R 181 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8213 (tt0) outliers start: 11 outliers final: 9 residues processed: 48 average time/residue: 0.1253 time to fit residues: 7.2912 Evaluate side-chains 47 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2295 Z= 0.166 Angle : 0.511 6.018 3131 Z= 0.248 Chirality : 0.039 0.160 368 Planarity : 0.003 0.030 361 Dihedral : 8.199 53.248 380 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.15 % Allowed : 27.80 % Favored : 68.05 % 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: 2.96 (0.53), residues: 269 helix: 2.80 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.51 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 64 TYR 0.010 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.274 Fit side-chains REVERT: R 38 LEU cc_start: 0.8824 (tp) cc_final: 0.8585 (tp) REVERT: R 75 ASP cc_start: 0.8561 (m-30) cc_final: 0.8229 (t0) REVERT: R 166 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8461 (tptt) REVERT: R 181 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: R 201 SER cc_start: 0.9098 (m) cc_final: 0.8600 (p) outliers start: 10 outliers final: 9 residues processed: 45 average time/residue: 0.1114 time to fit residues: 6.2507 Evaluate side-chains 45 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU 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: 0.5980 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2295 Z= 0.169 Angle : 0.517 6.002 3131 Z= 0.251 Chirality : 0.039 0.160 368 Planarity : 0.003 0.030 361 Dihedral : 8.036 52.660 380 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.56 % Allowed : 28.63 % Favored : 66.80 % 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: 3.05 (0.54), residues: 269 helix: 2.86 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.47 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 64 TYR 0.010 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.276 Fit side-chains REVERT: R 38 LEU cc_start: 0.8807 (tp) cc_final: 0.8606 (tp) REVERT: R 75 ASP cc_start: 0.8559 (m-30) cc_final: 0.8243 (t0) REVERT: R 166 LYS cc_start: 0.9081 (ttpp) cc_final: 0.8429 (tptt) REVERT: R 181 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: R 201 SER cc_start: 0.9144 (m) cc_final: 0.8655 (p) REVERT: R 242 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8621 (pp30) outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 0.1153 time to fit residues: 6.2847 Evaluate side-chains 46 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 242 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2295 Z= 0.172 Angle : 0.512 6.029 3131 Z= 0.250 Chirality : 0.039 0.160 368 Planarity : 0.003 0.030 361 Dihedral : 7.993 52.442 380 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.15 % Allowed : 28.63 % Favored : 67.22 % 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: 3.05 (0.53), residues: 269 helix: 2.85 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.45 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.005 0.001 PHE R 64 TYR 0.010 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.410 Fit side-chains REVERT: R 38 LEU cc_start: 0.8791 (tp) cc_final: 0.8566 (tp) REVERT: R 75 ASP cc_start: 0.8570 (m-30) cc_final: 0.8256 (t0) REVERT: R 166 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8419 (tptt) REVERT: R 181 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: R 201 SER cc_start: 0.9166 (m) cc_final: 0.8654 (p) REVERT: R 242 GLN cc_start: 0.8890 (pp30) cc_final: 0.8638 (pp30) outliers start: 10 outliers final: 9 residues processed: 44 average time/residue: 0.1072 time to fit residues: 6.0275 Evaluate side-chains 45 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 174 ASP Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.107643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.083035 restraints weight = 3796.708| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.20 r_work: 0.2864 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2295 Z= 0.154 Angle : 0.502 5.941 3131 Z= 0.245 Chirality : 0.039 0.164 368 Planarity : 0.003 0.029 361 Dihedral : 7.614 51.173 380 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.15 % Allowed : 28.63 % Favored : 67.22 % 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: 3.08 (0.53), residues: 269 helix: 2.88 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.48 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 64 TYR 0.009 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 912.47 seconds wall clock time: 17 minutes 42.14 seconds (1062.14 seconds total)