Starting phenix.real_space_refine on Thu Jul 18 18:04:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/07_2024/7vv6_32139.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/07_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_32139/07_2024/7vv6_32139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/07_2024/7vv6_32139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/07_2024/7vv6_32139.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/07_2024/7vv6_32139.cif" } 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-5388/modules/chem_data/mon_lib" Total number of atoms: 2227 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2161 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.16, per 1000 atoms: 0.97 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: 1.48 Conformation dependent library (CDL) restraints added in 482.4 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... Secondary structure from input PDB file: 12 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.529A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 94 removed outlier: 3.831A pdb=" N VAL R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) 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 104 through 133 removed outlier: 3.602A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 212 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 217 through 236 Processing helix chain 'R' and resid 236 through 245 removed outlier: 4.339A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 286 through 288 No H-bonds generated for 'chain 'R' and resid 286 through 288' 169 hydrogen bonds defined for protein. 507 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: 0.59 Time building geometry restraints manager: 0.93 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: 1941 3.33 - 3.86: 3854 3.86 - 4.38: 4171 4.38 - 4.90: 7427 Nonbonded interactions: 18022 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 18017 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: 0.210 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.890 Find NCS groups from input model: 0.010 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.860 ------------------------------------------------------------------------------- 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= 0.620 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 : 0.280 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: 0.1215 time to fit residues: 9.8266 Evaluate side-chains 31 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 ASN R 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2295 Z= 0.162 Angle : 0.626 8.953 3131 Z= 0.299 Chirality : 0.042 0.229 368 Planarity : 0.005 0.035 361 Dihedral : 10.642 59.032 380 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.15 % Allowed : 28.22 % Favored : 67.63 % 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: 0.24 (0.49), residues: 269 helix: 0.69 (0.34), residues: 219 sheet: None (None), residues: 0 loop : -1.98 (0.80), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 248 HIS 0.003 0.001 HIS R 144 PHE 0.009 0.001 PHE R 183 TYR 0.012 0.002 TYR R 222 ARG 0.012 0.001 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 42 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.258 Fit side-chains REVERT: R 59 MET cc_start: 0.8211 (mtt) cc_final: 0.7847 (mtt) REVERT: R 166 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8252 (tptt) outliers start: 10 outliers final: 5 residues processed: 42 average time/residue: 0.1125 time to fit residues: 5.8285 Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 0.0030 chunk 18 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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: 0.8165 moved from start: 0.2901 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= 0.158 Angle : 0.562 6.002 3131 Z= 0.272 Chirality : 0.040 0.141 368 Planarity : 0.003 0.031 361 Dihedral : 9.068 57.576 380 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.90 % Allowed : 27.80 % 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: 1.75 (0.52), residues: 269 helix: 1.83 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -2.19 (0.79), residues: 47 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 0.009 0.001 PHE R 183 TYR 0.009 0.001 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 40 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.249 Fit side-chains REVERT: R 59 MET cc_start: 0.8232 (mtt) cc_final: 0.7880 (mtt) REVERT: R 166 LYS cc_start: 0.8906 (ttpp) cc_final: 0.8305 (tptt) REVERT: R 242 GLN cc_start: 0.8769 (pp30) cc_final: 0.8421 (pp30) outliers start: 7 outliers final: 6 residues processed: 38 average time/residue: 0.1274 time to fit residues: 5.9681 Evaluate side-chains 35 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain R residue 174 ASP 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: 0.7980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 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: 0.8195 moved from start: 0.3197 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= 0.172 Angle : 0.539 6.093 3131 Z= 0.262 Chirality : 0.040 0.157 368 Planarity : 0.003 0.031 361 Dihedral : 8.871 54.729 380 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.98 % Allowed : 26.14 % 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: 2.42 (0.53), residues: 269 helix: 2.28 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -1.63 (0.87), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 250 HIS 0.001 0.000 HIS R 261 PHE 0.007 0.001 PHE R 183 TYR 0.014 0.001 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 44 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 0.260 Fit side-chains REVERT: R 38 LEU cc_start: 0.8833 (tp) cc_final: 0.8555 (tp) REVERT: R 59 MET cc_start: 0.8232 (mtt) cc_final: 0.7890 (mtt) REVERT: R 163 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8466 (tt) REVERT: R 166 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8384 (tptt) REVERT: R 181 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: R 201 SER cc_start: 0.9105 (m) cc_final: 0.8600 (p) REVERT: R 242 GLN cc_start: 0.8810 (pp30) cc_final: 0.8522 (pp30) outliers start: 12 outliers final: 8 residues processed: 43 average time/residue: 0.1152 time to fit residues: 6.1049 Evaluate side-chains 41 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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: 0.8227 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2295 Z= 0.229 Angle : 0.551 6.328 3131 Z= 0.270 Chirality : 0.041 0.154 368 Planarity : 0.003 0.031 361 Dihedral : 9.156 58.761 380 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.98 % Allowed : 25.31 % 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: 2.59 (0.53), residues: 269 helix: 2.36 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -1.37 (0.90), residues: 50 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 183 TYR 0.014 0.002 TYR R 222 ARG 0.001 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 44 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 0.251 Fit side-chains REVERT: R 59 MET cc_start: 0.8194 (mtt) cc_final: 0.7850 (mtt) REVERT: R 75 ASP cc_start: 0.8535 (m-30) cc_final: 0.8151 (t0) REVERT: R 166 LYS cc_start: 0.8975 (ttpp) cc_final: 0.8432 (tptt) REVERT: R 181 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: R 242 GLN cc_start: 0.8839 (pp30) cc_final: 0.8533 (pp30) outliers start: 12 outliers final: 10 residues processed: 42 average time/residue: 0.1263 time to fit residues: 6.4790 Evaluate side-chains 41 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 30 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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: 0.8181 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2295 Z= 0.137 Angle : 0.521 5.883 3131 Z= 0.254 Chirality : 0.039 0.162 368 Planarity : 0.003 0.030 361 Dihedral : 8.572 58.642 380 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.07 % Allowed : 29.05 % 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: 2.92 (0.53), residues: 269 helix: 2.81 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.70 (0.82), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.000 0.000 HIS R 261 PHE 0.006 0.001 PHE R 64 TYR 0.012 0.002 TYR R 222 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 38 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.246 Fit side-chains REVERT: R 38 LEU cc_start: 0.8829 (tp) cc_final: 0.8557 (tp) REVERT: R 59 MET cc_start: 0.8123 (mtt) cc_final: 0.7763 (mtt) REVERT: R 166 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8405 (tptt) REVERT: R 242 GLN cc_start: 0.8852 (pp30) cc_final: 0.8547 (pp30) outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.1224 time to fit residues: 5.7191 Evaluate side-chains 37 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 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 182 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.0370 chunk 12 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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: 0.8184 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2295 Z= 0.147 Angle : 0.512 5.928 3131 Z= 0.251 Chirality : 0.039 0.161 368 Planarity : 0.003 0.029 361 Dihedral : 8.391 55.135 380 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: 3.03 (0.53), residues: 269 helix: 2.89 (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 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 144 PHE 0.007 0.001 PHE R 64 TYR 0.011 0.002 TYR R 222 ARG 0.002 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 46 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.222 Fit side-chains REVERT: R 38 LEU cc_start: 0.8832 (tp) cc_final: 0.8523 (tp) REVERT: R 59 MET cc_start: 0.8104 (mtt) cc_final: 0.7735 (mtt) REVERT: R 75 ASP cc_start: 0.8563 (m-30) cc_final: 0.8247 (t0) REVERT: R 163 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8419 (tt) REVERT: R 166 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8375 (tptt) REVERT: R 201 SER cc_start: 0.9080 (m) cc_final: 0.8598 (p) REVERT: R 242 GLN cc_start: 0.8848 (pp30) cc_final: 0.8522 (pp30) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.1246 time to fit residues: 6.8259 Evaluate side-chains 40 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 182 THR 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: 0.5980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2295 Z= 0.169 Angle : 0.535 6.030 3131 Z= 0.261 Chirality : 0.040 0.159 368 Planarity : 0.003 0.029 361 Dihedral : 8.274 52.867 380 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.73 % Allowed : 28.63 % Favored : 67.63 % 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: 3.04 (0.53), residues: 269 helix: 2.88 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.62 (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 144 PHE 0.006 0.001 PHE R 64 TYR 0.012 0.002 TYR R 222 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 44 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.255 Fit side-chains REVERT: R 38 LEU cc_start: 0.8835 (tp) cc_final: 0.8532 (tp) REVERT: R 59 MET cc_start: 0.8082 (mtt) cc_final: 0.7717 (mtt) REVERT: R 75 ASP cc_start: 0.8567 (m-30) cc_final: 0.8251 (t0) REVERT: R 166 LYS cc_start: 0.8964 (ttpp) cc_final: 0.8399 (tptt) REVERT: R 201 SER cc_start: 0.9095 (m) cc_final: 0.8607 (p) REVERT: R 242 GLN cc_start: 0.8851 (pp30) cc_final: 0.8530 (pp30) outliers start: 9 outliers final: 9 residues processed: 43 average time/residue: 0.1101 time to fit residues: 5.9346 Evaluate side-chains 43 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8199 moved from start: 0.3881 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= 0.179 Angle : 0.535 6.063 3131 Z= 0.263 Chirality : 0.040 0.160 368 Planarity : 0.003 0.029 361 Dihedral : 8.184 52.356 380 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.15 % Allowed : 28.22 % Favored : 67.63 % 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: 3.11 (0.54), residues: 269 helix: 2.93 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.62 (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 183 TYR 0.012 0.002 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 43 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.233 Fit side-chains REVERT: R 38 LEU cc_start: 0.8841 (tp) cc_final: 0.8624 (tp) REVERT: R 59 MET cc_start: 0.8074 (mtt) cc_final: 0.7712 (mtt) REVERT: R 75 ASP cc_start: 0.8562 (m-30) cc_final: 0.8233 (t0) REVERT: R 166 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8399 (tptt) REVERT: R 181 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: R 201 SER cc_start: 0.9151 (m) cc_final: 0.8662 (p) REVERT: R 242 GLN cc_start: 0.8853 (pp30) cc_final: 0.8527 (pp30) outliers start: 10 outliers final: 9 residues processed: 42 average time/residue: 0.1016 time to fit residues: 5.3533 Evaluate side-chains 43 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8185 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2295 Z= 0.155 Angle : 0.525 5.941 3131 Z= 0.257 Chirality : 0.039 0.163 368 Planarity : 0.003 0.029 361 Dihedral : 7.874 51.667 380 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.15 % Allowed : 28.22 % Favored : 67.63 % 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: 3.23 (0.54), residues: 269 helix: 3.02 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.58 (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 144 PHE 0.006 0.001 PHE R 64 TYR 0.011 0.002 TYR R 222 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 43 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.265 Fit side-chains REVERT: R 38 LEU cc_start: 0.8820 (tp) cc_final: 0.8606 (tp) REVERT: R 75 ASP cc_start: 0.8589 (m-30) cc_final: 0.8254 (t0) REVERT: R 163 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8420 (tt) REVERT: R 166 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8414 (tptt) REVERT: R 181 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: R 201 SER cc_start: 0.9139 (m) cc_final: 0.8643 (p) REVERT: R 242 GLN cc_start: 0.8848 (pp30) cc_final: 0.8518 (pp30) outliers start: 10 outliers final: 8 residues processed: 43 average time/residue: 0.1161 time to fit residues: 6.2072 Evaluate side-chains 43 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 152 LEU 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: 1.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.107767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.081648 restraints weight = 3723.288| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.24 r_work: 0.2827 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2295 Z= 0.161 Angle : 0.526 5.980 3131 Z= 0.257 Chirality : 0.039 0.162 368 Planarity : 0.003 0.030 361 Dihedral : 7.762 51.391 380 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: 3.21 (0.54), residues: 269 helix: 3.01 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -1.58 (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 0.005 0.001 PHE R 64 TYR 0.011 0.002 TYR R 222 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: 901.40 seconds wall clock time: 18 minutes 43.73 seconds (1123.73 seconds total)