Starting phenix.real_space_refine on Fri Apr 5 16:12:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj8_36342/04_2024/8jj8_36342_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj8_36342/04_2024/8jj8_36342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj8_36342/04_2024/8jj8_36342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj8_36342/04_2024/8jj8_36342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj8_36342/04_2024/8jj8_36342_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj8_36342/04_2024/8jj8_36342_updated.pdb" } resolution = 3.2 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= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 707 atoms to isotropic. 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 20 5.16 5 C 1984 2.51 5 N 488 2.21 5 O 531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 335": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3023 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2998 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 8, 'TRANS': 366} Chain breaks: 1 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H98': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.74 Number of scatterers: 3023 At special positions: 0 Unit cell: (57.78, 103.79, 82.39, 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 20 16.00 O 531 8.00 N 488 7.00 C 1984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 106 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 190 " 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: 1.28 Conformation dependent library (CDL) restraints added in 538.6 milliseconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'F' and resid 31 through 55 removed outlier: 4.023A pdb=" N MET F 36 " --> pdb=" O TRP F 32 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 92 removed outlier: 3.531A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL F 87 " --> pdb=" O GLY F 83 " (cutoff:3.500A) Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 103 through 135 Processing helix chain 'F' and resid 138 through 143 removed outlier: 4.230A pdb=" N SER F 143 " --> pdb=" O PHE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 165 Processing helix chain 'F' and resid 167 through 170 No H-bonds generated for 'chain 'F' and resid 167 through 170' Processing helix chain 'F' and resid 179 through 185 removed outlier: 3.780A pdb=" N ASN F 183 " --> pdb=" O GLN F 179 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 207 Processing helix chain 'F' and resid 209 through 248 Processing helix chain 'F' and resid 253 through 272 Processing helix chain 'F' and resid 279 through 304 Processing helix chain 'F' and resid 307 through 364 removed outlier: 4.741A pdb=" N GLN F 326 " --> pdb=" O ASN F 322 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU F 329 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Proline residue: F 355 - end of helix removed outlier: 3.920A pdb=" N ILE F 361 " --> pdb=" O PHE F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 369 No H-bonds generated for 'chain 'F' and resid 367 through 369' Processing helix chain 'F' and resid 372 through 393 removed outlier: 3.909A pdb=" N ASN F 385 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER F 386 " --> pdb=" O GLY F 382 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY F 387 " --> pdb=" O TYR F 383 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE F 388 " --> pdb=" O VAL F 384 " (cutoff:3.500A) Proline residue: F 390 - end of helix Processing helix chain 'F' and resid 397 through 406 removed outlier: 3.590A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 669 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: 0.78 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 478 1.29 - 1.42: 820 1.42 - 1.55: 1760 1.55 - 1.68: 2 1.68 - 1.81: 31 Bond restraints: 3091 Sorted by residual: bond pdb=" C TYR F 328 " pdb=" O TYR F 328 " ideal model delta sigma weight residual 1.236 1.161 0.076 1.26e-02 6.30e+03 3.61e+01 bond pdb=" C LYS F 327 " pdb=" O LYS F 327 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.16e-02 7.43e+03 1.61e+01 bond pdb=" C GLN F 326 " pdb=" O GLN F 326 " ideal model delta sigma weight residual 1.235 1.286 -0.050 1.26e-02 6.30e+03 1.60e+01 bond pdb=" C LEU F 342 " pdb=" O LEU F 342 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.26e-02 6.30e+03 1.27e+01 bond pdb=" C ALA F 338 " pdb=" O ALA F 338 " ideal model delta sigma weight residual 1.236 1.281 -0.045 1.29e-02 6.01e+03 1.22e+01 ... (remaining 3086 not shown) Histogram of bond angle deviations from ideal: 93.38 - 101.51: 12 101.51 - 109.64: 246 109.64 - 117.77: 2050 117.77 - 125.89: 1834 125.89 - 134.02: 54 Bond angle restraints: 4196 Sorted by residual: angle pdb=" O ILE F 325 " pdb=" C ILE F 325 " pdb=" N GLN F 326 " ideal model delta sigma weight residual 121.96 130.61 -8.65 8.40e-01 1.42e+00 1.06e+02 angle pdb=" CA ILE F 325 " pdb=" C ILE F 325 " pdb=" N GLN F 326 " ideal model delta sigma weight residual 115.25 106.83 8.42 9.50e-01 1.11e+00 7.85e+01 angle pdb=" N LYS F 340 " pdb=" CA LYS F 340 " pdb=" C LYS F 340 " ideal model delta sigma weight residual 111.28 102.34 8.94 1.09e+00 8.42e-01 6.73e+01 angle pdb=" N GLN F 326 " pdb=" CA GLN F 326 " pdb=" C GLN F 326 " ideal model delta sigma weight residual 110.80 93.38 17.42 2.13e+00 2.20e-01 6.69e+01 angle pdb=" N LEU F 329 " pdb=" CA LEU F 329 " pdb=" C LEU F 329 " ideal model delta sigma weight residual 111.07 103.97 7.10 1.07e+00 8.73e-01 4.41e+01 ... (remaining 4191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1615 17.82 - 35.64: 168 35.64 - 53.46: 33 53.46 - 71.28: 4 71.28 - 89.10: 6 Dihedral angle restraints: 1826 sinusoidal: 718 harmonic: 1108 Sorted by residual: dihedral pdb=" CB CYS F 106 " pdb=" SG CYS F 106 " pdb=" SG CYS F 191 " pdb=" CB CYS F 191 " ideal model delta sinusoidal sigma weight residual -86.00 -175.10 89.10 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CA MET F 96 " pdb=" C MET F 96 " pdb=" N LYS F 97 " pdb=" CA LYS F 97 " ideal model delta harmonic sigma weight residual 180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" N GLN F 326 " pdb=" C GLN F 326 " pdb=" CA GLN F 326 " pdb=" CB GLN F 326 " ideal model delta harmonic sigma weight residual 122.80 114.83 7.97 0 2.50e+00 1.60e-01 1.02e+01 ... (remaining 1823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 399 0.060 - 0.120: 80 0.120 - 0.180: 6 0.180 - 0.240: 2 0.240 - 0.300: 2 Chirality restraints: 489 Sorted by residual: chirality pdb=" CA GLN F 326 " pdb=" N GLN F 326 " pdb=" C GLN F 326 " pdb=" CB GLN F 326 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LYS F 340 " pdb=" N LYS F 340 " pdb=" C LYS F 340 " pdb=" CB LYS F 340 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA LEU F 339 " pdb=" N LEU F 339 " pdb=" C LEU F 339 " pdb=" CB LEU F 339 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 486 not shown) Planarity restraints: 515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 326 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLN F 326 " -0.073 2.00e-02 2.50e+03 pdb=" O GLN F 326 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS F 327 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 329 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU F 329 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU F 329 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS F 330 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 236 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C ASN F 236 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN F 236 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP F 237 " 0.016 2.00e-02 2.50e+03 ... (remaining 512 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 58 2.67 - 3.22: 3128 3.22 - 3.78: 4803 3.78 - 4.34: 6205 4.34 - 4.90: 10175 Nonbonded interactions: 24369 Sorted by model distance: nonbonded pdb=" OE2 GLU F 187 " pdb=" OG1 THR F 189 " model vdw 2.107 2.440 nonbonded pdb=" OG SER F 203 " pdb=" O2 H98 F 501 " model vdw 2.191 2.440 nonbonded pdb=" O THR F 341 " pdb=" C LEU F 342 " model vdw 2.229 3.270 nonbonded pdb=" O THR F 239 " pdb=" ND2 ASN F 243 " model vdw 2.315 2.520 nonbonded pdb=" OD2 ASP F 113 " pdb=" OH TYR F 383 " model vdw 2.323 2.440 ... (remaining 24364 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 4.930 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.650 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 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 : 0.005 0.076 3091 Z= 0.316 Angle : 0.898 17.416 4196 Z= 0.612 Chirality : 0.050 0.300 489 Planarity : 0.005 0.042 515 Dihedral : 15.213 81.138 1098 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.86 % Allowed : 1.55 % Favored : 96.59 % 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: 0.54 (0.45), residues: 371 helix: 1.06 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -3.25 (0.85), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.021 0.002 PHE F 284 TYR 0.020 0.002 TYR F 328 ARG 0.007 0.001 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.328 Fit side-chains REVERT: F 230 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7669 (tp) REVERT: F 269 ASP cc_start: 0.7008 (m-30) cc_final: 0.6792 (m-30) REVERT: F 331 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6948 (t80) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.1317 time to fit residues: 12.6939 Evaluate side-chains 63 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 332 CYS Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN F 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3091 Z= 0.232 Angle : 0.596 6.081 4196 Z= 0.316 Chirality : 0.042 0.171 489 Planarity : 0.003 0.024 515 Dihedral : 9.740 77.837 422 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.86 % Allowed : 7.74 % Favored : 90.40 % 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: 0.99 (0.44), residues: 371 helix: 1.44 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.25 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 237 HIS 0.002 0.001 HIS F 93 PHE 0.015 0.002 PHE F 284 TYR 0.020 0.002 TYR F 328 ARG 0.005 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.391 Fit side-chains REVERT: F 122 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7415 (mm-30) REVERT: F 269 ASP cc_start: 0.7003 (m-30) cc_final: 0.6784 (m-30) outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 0.1070 time to fit residues: 9.8717 Evaluate side-chains 54 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN F 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3091 Z= 0.189 Angle : 0.546 6.640 4196 Z= 0.288 Chirality : 0.039 0.143 489 Planarity : 0.003 0.021 515 Dihedral : 8.086 80.226 413 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.79 % Allowed : 10.22 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.42 (0.45), residues: 371 helix: 1.75 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.19 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 237 HIS 0.002 0.001 HIS F 363 PHE 0.015 0.001 PHE F 284 TYR 0.022 0.002 TYR F 324 ARG 0.003 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.339 Fit side-chains REVERT: F 130 ASP cc_start: 0.7764 (t0) cc_final: 0.7450 (t0) REVERT: F 269 ASP cc_start: 0.6965 (m-30) cc_final: 0.6732 (m-30) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.0923 time to fit residues: 8.2700 Evaluate side-chains 55 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 ASN F 243 ASN F 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3091 Z= 0.218 Angle : 0.556 6.855 4196 Z= 0.296 Chirality : 0.039 0.164 489 Planarity : 0.003 0.024 515 Dihedral : 7.899 80.156 413 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.17 % Allowed : 13.31 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.48 (0.44), residues: 371 helix: 1.85 (0.29), residues: 302 sheet: None (None), residues: 0 loop : -3.14 (0.69), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 237 HIS 0.001 0.000 HIS F 363 PHE 0.013 0.002 PHE F 284 TYR 0.015 0.002 TYR F 324 ARG 0.002 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.265 Fit side-chains REVERT: F 130 ASP cc_start: 0.7748 (t0) cc_final: 0.7448 (t0) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 0.1013 time to fit residues: 7.1149 Evaluate side-chains 49 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 183 ASN Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 404 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3091 Z= 0.176 Angle : 0.517 6.456 4196 Z= 0.276 Chirality : 0.038 0.125 489 Planarity : 0.003 0.022 515 Dihedral : 7.597 79.016 412 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.79 % Allowed : 13.93 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.84 (0.45), residues: 371 helix: 2.12 (0.30), residues: 299 sheet: None (None), residues: 0 loop : -2.91 (0.74), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.014 0.001 PHE F 284 TYR 0.018 0.002 TYR F 324 ARG 0.002 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.363 Fit side-chains REVERT: F 122 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7500 (mm-30) REVERT: F 130 ASP cc_start: 0.7649 (t0) cc_final: 0.7396 (t0) REVERT: F 342 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6160 (mp) outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.1116 time to fit residues: 8.3884 Evaluate side-chains 55 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 183 ASN Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.0010 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 404 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3091 Z= 0.169 Angle : 0.534 6.943 4196 Z= 0.281 Chirality : 0.038 0.114 489 Planarity : 0.003 0.021 515 Dihedral : 7.545 78.438 412 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.41 % Allowed : 14.86 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.45), residues: 371 helix: 2.14 (0.30), residues: 299 sheet: None (None), residues: 0 loop : -2.80 (0.75), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.014 0.001 PHE F 284 TYR 0.020 0.002 TYR F 324 ARG 0.002 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.324 Fit side-chains REVERT: F 122 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7369 (mm-30) REVERT: F 269 ASP cc_start: 0.6970 (m-30) cc_final: 0.6759 (m-30) REVERT: F 342 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6205 (mp) outliers start: 11 outliers final: 7 residues processed: 60 average time/residue: 0.1006 time to fit residues: 8.0582 Evaluate side-chains 59 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 183 ASN Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 404 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3091 Z= 0.177 Angle : 0.544 7.233 4196 Z= 0.285 Chirality : 0.039 0.219 489 Planarity : 0.003 0.021 515 Dihedral : 7.538 77.996 412 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.72 % Allowed : 15.17 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.45), residues: 371 helix: 2.12 (0.30), residues: 300 sheet: None (None), residues: 0 loop : -2.79 (0.75), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 PHE 0.016 0.001 PHE F 284 TYR 0.023 0.002 TYR F 324 ARG 0.002 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.349 Fit side-chains REVERT: F 342 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6237 (mp) outliers start: 12 outliers final: 8 residues processed: 54 average time/residue: 0.1047 time to fit residues: 7.6987 Evaluate side-chains 57 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 332 CYS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3091 Z= 0.187 Angle : 0.545 6.690 4196 Z= 0.289 Chirality : 0.040 0.217 489 Planarity : 0.003 0.022 515 Dihedral : 7.584 78.114 412 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.41 % Allowed : 16.41 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.80 (0.45), residues: 371 helix: 2.06 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -2.84 (0.74), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 237 HIS 0.001 0.000 HIS F 363 PHE 0.016 0.001 PHE F 284 TYR 0.027 0.002 TYR F 324 ARG 0.002 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.416 Fit side-chains REVERT: F 342 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6232 (mp) outliers start: 11 outliers final: 9 residues processed: 51 average time/residue: 0.1071 time to fit residues: 7.5803 Evaluate side-chains 54 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 125 CYS Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 332 CYS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7273 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3091 Z= 0.187 Angle : 0.556 7.069 4196 Z= 0.291 Chirality : 0.039 0.203 489 Planarity : 0.003 0.022 515 Dihedral : 7.608 78.115 412 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.10 % Allowed : 16.41 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.92 (0.45), residues: 371 helix: 2.14 (0.29), residues: 298 sheet: None (None), residues: 0 loop : -2.62 (0.77), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 237 HIS 0.001 0.000 HIS F 363 PHE 0.017 0.001 PHE F 284 TYR 0.029 0.002 TYR F 324 ARG 0.001 0.000 ARG F 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.374 Fit side-chains REVERT: F 342 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6216 (mp) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.1067 time to fit residues: 6.9256 Evaluate side-chains 46 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 332 CYS Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3091 Z= 0.196 Angle : 0.561 6.838 4196 Z= 0.295 Chirality : 0.040 0.203 489 Planarity : 0.003 0.022 515 Dihedral : 7.663 78.221 412 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.48 % Allowed : 17.34 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.87 (0.45), residues: 371 helix: 2.11 (0.29), residues: 298 sheet: None (None), residues: 0 loop : -2.63 (0.77), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 237 HIS 0.001 0.000 HIS F 363 PHE 0.016 0.001 PHE F 284 TYR 0.032 0.002 TYR F 324 ARG 0.002 0.000 ARG F 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.309 Fit side-chains REVERT: F 122 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7031 (mm-30) REVERT: F 342 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6191 (mp) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.0994 time to fit residues: 6.4262 Evaluate side-chains 48 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 332 CYS Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.191398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149722 restraints weight = 3760.180| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.74 r_work: 0.3597 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3091 Z= 0.194 Angle : 0.568 7.028 4196 Z= 0.296 Chirality : 0.040 0.200 489 Planarity : 0.003 0.021 515 Dihedral : 7.664 78.231 412 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.86 % Allowed : 18.89 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.83 (0.45), residues: 371 helix: 2.10 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -2.93 (0.77), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 237 HIS 0.001 0.000 HIS F 363 PHE 0.017 0.001 PHE F 284 TYR 0.031 0.002 TYR F 324 ARG 0.002 0.000 ARG F 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1105.96 seconds wall clock time: 20 minutes 35.57 seconds (1235.57 seconds total)