Starting phenix.real_space_refine on Thu Nov 14 00:55:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/11_2024/8jjo_36361_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/11_2024/8jjo_36361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/11_2024/8jjo_36361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/11_2024/8jjo_36361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/11_2024/8jjo_36361_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/11_2024/8jjo_36361_neut.cif" } resolution = 3.4 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= -0.002 sd= 0.158 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 20 5.16 5 C 1980 2.51 5 N 487 2.21 5 O 529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3016 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: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'JTZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.85 Number of scatterers: 3016 At special positions: 0 Unit cell: (54.57, 81.32, 107, 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 529 8.00 N 487 7.00 C 1980 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 354.5 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... Secondary structure from input PDB file: 15 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'F' and resid 29 through 61 removed outlier: 3.703A pdb=" N VAL F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY F 37 " --> pdb=" O VAL F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 86 Processing helix chain 'F' and resid 86 through 96 Processing helix chain 'F' and resid 106 through 134 Processing helix chain 'F' and resid 146 through 170 removed outlier: 4.093A pdb=" N LEU F 167 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Proline residue: F 168 - end of helix Processing helix chain 'F' and resid 180 through 186 removed outlier: 3.816A pdb=" N ASN F 183 " --> pdb=" O GLU F 180 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA F 186 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 210 through 237 removed outlier: 3.560A pdb=" N VAL F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS F 227 " --> pdb=" O PHE F 223 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG F 228 " --> pdb=" O GLN F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 247 Processing helix chain 'F' and resid 252 through 273 Processing helix chain 'F' and resid 279 through 300 Processing helix chain 'F' and resid 309 through 366 removed outlier: 4.393A pdb=" N GLN F 326 " --> pdb=" O ASN F 322 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS F 340 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR F 350 " --> pdb=" O MET F 346 " (cutoff:3.500A) Proline residue: F 355 - end of helix removed outlier: 3.506A pdb=" N VAL F 359 " --> pdb=" O PRO F 355 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE F 361 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL F 362 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL F 364 " --> pdb=" O ASN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 removed outlier: 3.909A pdb=" N GLY F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER F 386 " --> pdb=" O GLY F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 394 removed outlier: 4.366A pdb=" N LEU F 391 " --> pdb=" O GLY F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 405 removed outlier: 3.525A pdb=" N ALA F 402 " --> pdb=" O ASP F 398 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 663 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: 0.74 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 930 1.34 - 1.46: 738 1.46 - 1.58: 1384 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 3083 Sorted by residual: bond pdb=" C12 JTZ F 501 " pdb=" C7 JTZ F 501 " ideal model delta sigma weight residual 1.403 1.353 0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C2 JTZ F 501 " pdb=" N1 JTZ F 501 " ideal model delta sigma weight residual 1.458 1.417 0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" C8 JTZ F 501 " pdb=" C9 JTZ F 501 " ideal model delta sigma weight residual 1.390 1.352 0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" C7 JTZ F 501 " pdb=" C8 JTZ F 501 " ideal model delta sigma weight residual 1.393 1.357 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" C10 JTZ F 501 " pdb=" C9 JTZ F 501 " ideal model delta sigma weight residual 1.385 1.351 0.034 2.00e-02 2.50e+03 2.88e+00 ... (remaining 3078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 4105 1.78 - 3.56: 58 3.56 - 5.35: 11 5.35 - 7.13: 6 7.13 - 8.91: 4 Bond angle restraints: 4184 Sorted by residual: angle pdb=" C1 JTZ F 501 " pdb=" C2 JTZ F 501 " pdb=" N1 JTZ F 501 " ideal model delta sigma weight residual 114.33 105.42 8.91 3.00e+00 1.11e-01 8.83e+00 angle pdb=" C2 JTZ F 501 " pdb=" N1 JTZ F 501 " pdb=" C4 JTZ F 501 " ideal model delta sigma weight residual 115.12 106.67 8.45 3.00e+00 1.11e-01 7.93e+00 angle pdb=" N TRP F 105 " pdb=" CA TRP F 105 " pdb=" C TRP F 105 " ideal model delta sigma weight residual 113.38 110.14 3.24 1.17e+00 7.31e-01 7.69e+00 angle pdb=" C ASP F 367 " pdb=" N ASN F 368 " pdb=" CA ASN F 368 " ideal model delta sigma weight residual 121.54 126.63 -5.09 1.91e+00 2.74e-01 7.09e+00 angle pdb=" C6 JTZ F 501 " pdb=" C5 JTZ F 501 " pdb=" O1 JTZ F 501 " ideal model delta sigma weight residual 112.06 104.46 7.60 3.00e+00 1.11e-01 6.42e+00 ... (remaining 4179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 1729 31.27 - 62.54: 83 62.54 - 93.82: 8 93.82 - 125.09: 0 125.09 - 156.36: 1 Dihedral angle restraints: 1821 sinusoidal: 713 harmonic: 1108 Sorted by residual: dihedral pdb=" CB CYS F 184 " pdb=" SG CYS F 184 " pdb=" SG CYS F 190 " pdb=" CB CYS F 190 " ideal model delta sinusoidal sigma weight residual -86.00 0.68 -86.68 1 1.00e+01 1.00e-02 9.04e+01 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 -162.86 76.86 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" C4 JTZ F 501 " pdb=" C5 JTZ F 501 " pdb=" C6 JTZ F 501 " pdb=" O2 JTZ F 501 " ideal model delta sinusoidal sigma weight residual 181.12 24.76 156.36 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 1818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 430 0.060 - 0.120: 56 0.120 - 0.181: 1 0.181 - 0.241: 0 0.241 - 0.301: 1 Chirality restraints: 488 Sorted by residual: chirality pdb=" C5 JTZ F 501 " pdb=" C4 JTZ F 501 " pdb=" C6 JTZ F 501 " pdb=" O1 JTZ F 501 " both_signs ideal model delta sigma weight residual False -2.33 -2.63 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE F 370 " pdb=" CA ILE F 370 " pdb=" CG1 ILE F 370 " pdb=" CG2 ILE F 370 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ASN F 368 " pdb=" N ASN F 368 " pdb=" C ASN F 368 " pdb=" CB ASN F 368 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 485 not shown) Planarity restraints: 513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 237 " 0.003 2.00e-02 2.50e+03 8.53e-03 1.82e+00 pdb=" CG TRP F 237 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP F 237 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP F 237 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 237 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP F 237 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 237 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 237 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 237 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 237 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 385 " 0.006 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" C ASN F 385 " -0.019 2.00e-02 2.50e+03 pdb=" O ASN F 385 " 0.007 2.00e-02 2.50e+03 pdb=" N SER F 386 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 354 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO F 355 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 355 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 355 " -0.015 5.00e-02 4.00e+02 ... (remaining 510 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 140 2.73 - 3.27: 3211 3.27 - 3.81: 5027 3.81 - 4.36: 5604 4.36 - 4.90: 9744 Nonbonded interactions: 23726 Sorted by model distance: nonbonded pdb=" OH TYR F 219 " pdb=" O LEU F 339 " model vdw 2.184 3.040 nonbonded pdb=" OD2 ASP F 113 " pdb=" OH TYR F 383 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR F 118 " pdb=" OG SER F 207 " model vdw 2.276 3.040 nonbonded pdb=" O ALA F 119 " pdb=" OG1 THR F 123 " model vdw 2.377 3.040 nonbonded pdb=" C4 JTZ F 501 " pdb=" O2 JTZ F 501 " model vdw 2.378 2.752 ... (remaining 23721 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: 0.460 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.710 Find NCS groups from input model: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 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 : 0.003 0.050 3083 Z= 0.234 Angle : 0.637 8.912 4184 Z= 0.328 Chirality : 0.041 0.301 488 Planarity : 0.003 0.027 513 Dihedral : 17.699 156.361 1093 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.31 % Allowed : 17.96 % Favored : 81.73 % 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: -0.11 (0.44), residues: 371 helix: 0.85 (0.31), residues: 293 sheet: None (None), residues: 0 loop : -3.64 (0.54), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 237 HIS 0.006 0.001 HIS F 286 PHE 0.007 0.001 PHE F 193 TYR 0.010 0.001 TYR F 383 ARG 0.004 0.000 ARG F 371 *********************** 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 54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.253 Fit side-chains REVERT: F 171 MET cc_start: 0.6084 (ppp) cc_final: 0.5567 (ppp) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.1133 time to fit residues: 7.8587 Evaluate side-chains 54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 223 PHE 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: 0.6980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN F 360 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3083 Z= 0.202 Angle : 0.529 5.779 4184 Z= 0.282 Chirality : 0.039 0.127 488 Planarity : 0.003 0.027 513 Dihedral : 8.791 121.358 409 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.10 % Allowed : 17.03 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.45), residues: 371 helix: 1.19 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.48 (0.64), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 237 HIS 0.003 0.001 HIS F 286 PHE 0.008 0.001 PHE F 356 TYR 0.020 0.002 TYR F 383 ARG 0.002 0.000 ARG F 371 *********************** 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 67 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.349 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.1004 time to fit residues: 8.5742 Evaluate side-chains 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 386 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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: 0.6812 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3083 Z= 0.172 Angle : 0.495 7.113 4184 Z= 0.263 Chirality : 0.038 0.115 488 Planarity : 0.003 0.029 513 Dihedral : 8.419 112.106 409 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.41 % Allowed : 19.20 % Favored : 77.40 % 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: 0.78 (0.46), residues: 371 helix: 1.34 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.45 (0.65), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.003 0.001 HIS F 286 PHE 0.006 0.001 PHE F 356 TYR 0.010 0.001 TYR F 383 ARG 0.002 0.000 ARG F 371 *********************** 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 68 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.295 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.0969 time to fit residues: 8.1936 Evaluate side-chains 54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 325 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.0570 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 252 ASN ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3083 Z= 0.198 Angle : 0.521 9.613 4184 Z= 0.269 Chirality : 0.038 0.109 488 Planarity : 0.003 0.028 513 Dihedral : 8.195 109.011 409 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.79 % Allowed : 21.67 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.45), residues: 371 helix: 1.29 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.64 (0.58), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.002 0.001 HIS F 178 PHE 0.008 0.001 PHE F 288 TYR 0.024 0.002 TYR F 174 ARG 0.002 0.000 ARG F 371 *********************** 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 64 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.310 Fit side-chains REVERT: F 288 PHE cc_start: 0.7416 (m-80) cc_final: 0.7200 (m-80) outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.1035 time to fit residues: 8.5394 Evaluate side-chains 58 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.0000 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3083 Z= 0.169 Angle : 0.510 8.982 4184 Z= 0.264 Chirality : 0.037 0.116 488 Planarity : 0.003 0.028 513 Dihedral : 7.952 106.532 409 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.79 % Allowed : 22.91 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.46), residues: 371 helix: 1.40 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.69 (0.57), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 237 HIS 0.002 0.001 HIS F 178 PHE 0.009 0.001 PHE F 49 TYR 0.020 0.002 TYR F 174 ARG 0.001 0.000 ARG F 371 *********************** 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 63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.324 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 61 average time/residue: 0.1039 time to fit residues: 8.4822 Evaluate side-chains 58 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 374 VAL 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: 0.9980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3083 Z= 0.179 Angle : 0.511 9.397 4184 Z= 0.263 Chirality : 0.038 0.164 488 Planarity : 0.003 0.028 513 Dihedral : 7.862 106.589 409 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.10 % Allowed : 23.84 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.46), residues: 371 helix: 1.33 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.67 (0.56), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 380 HIS 0.002 0.001 HIS F 178 PHE 0.008 0.001 PHE F 288 TYR 0.017 0.002 TYR F 174 ARG 0.001 0.000 ARG F 371 *********************** 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 66 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.335 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.0948 time to fit residues: 8.0237 Evaluate side-chains 61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3083 Z= 0.173 Angle : 0.511 8.816 4184 Z= 0.262 Chirality : 0.038 0.137 488 Planarity : 0.003 0.029 513 Dihedral : 7.797 107.099 409 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.72 % Allowed : 23.84 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.46), residues: 371 helix: 1.36 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -3.63 (0.58), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 237 HIS 0.002 0.001 HIS F 178 PHE 0.008 0.001 PHE F 288 TYR 0.017 0.001 TYR F 174 ARG 0.003 0.000 ARG F 371 *********************** 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 63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.341 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.1135 time to fit residues: 8.8192 Evaluate side-chains 57 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 374 VAL 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: 0.4980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3083 Z= 0.187 Angle : 0.526 11.320 4184 Z= 0.267 Chirality : 0.038 0.129 488 Planarity : 0.003 0.029 513 Dihedral : 7.847 109.535 409 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.72 % Allowed : 24.15 % Favored : 72.14 % 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: 0.68 (0.46), residues: 371 helix: 1.31 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.66 (0.57), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 237 HIS 0.002 0.001 HIS F 178 PHE 0.008 0.001 PHE F 288 TYR 0.016 0.002 TYR F 174 ARG 0.001 0.000 ARG F 371 *********************** 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 65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.272 Fit side-chains REVERT: F 371 ARG cc_start: 0.6071 (ptp90) cc_final: 0.5862 (ptt-90) outliers start: 12 outliers final: 11 residues processed: 62 average time/residue: 0.1346 time to fit residues: 10.6083 Evaluate side-chains 62 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3083 Z= 0.265 Angle : 0.566 11.786 4184 Z= 0.286 Chirality : 0.040 0.121 488 Planarity : 0.003 0.028 513 Dihedral : 7.976 112.438 409 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.72 % Allowed : 24.15 % Favored : 72.14 % 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: 0.57 (0.45), residues: 371 helix: 1.17 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.32 (0.62), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 237 HIS 0.001 0.001 HIS F 178 PHE 0.010 0.001 PHE F 288 TYR 0.016 0.002 TYR F 383 ARG 0.002 0.000 ARG F 321 *********************** 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 65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.330 Fit side-chains REVERT: F 132 TYR cc_start: 0.6263 (t80) cc_final: 0.6020 (t80) REVERT: F 258 ASP cc_start: 0.6282 (t70) cc_final: 0.6064 (t0) outliers start: 12 outliers final: 12 residues processed: 62 average time/residue: 0.1296 time to fit residues: 10.2392 Evaluate side-chains 64 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.6846 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3083 Z= 0.182 Angle : 0.545 11.913 4184 Z= 0.275 Chirality : 0.038 0.119 488 Planarity : 0.003 0.029 513 Dihedral : 7.921 109.818 409 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.41 % Allowed : 24.46 % Favored : 72.14 % 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: 0.76 (0.45), residues: 371 helix: 1.37 (0.31), residues: 299 sheet: None (None), residues: 0 loop : -3.27 (0.55), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 237 HIS 0.001 0.000 HIS F 178 PHE 0.007 0.001 PHE F 49 TYR 0.017 0.001 TYR F 174 ARG 0.004 0.000 ARG F 371 ********************** 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 60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.327 Fit side-chains REVERT: F 258 ASP cc_start: 0.6257 (t70) cc_final: 0.6017 (t0) outliers start: 11 outliers final: 11 residues processed: 57 average time/residue: 0.1291 time to fit residues: 9.2346 Evaluate side-chains 58 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.204586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.162727 restraints weight = 3388.161| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.24 r_work: 0.3995 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3083 Z= 0.221 Angle : 0.568 10.066 4184 Z= 0.287 Chirality : 0.039 0.123 488 Planarity : 0.003 0.029 513 Dihedral : 8.001 111.615 409 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.72 % Allowed : 24.15 % Favored : 72.14 % 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: 0.86 (0.45), residues: 371 helix: 1.46 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -2.88 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 237 HIS 0.002 0.001 HIS F 172 PHE 0.009 0.001 PHE F 288 TYR 0.015 0.002 TYR F 383 ARG 0.004 0.000 ARG F 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1007.58 seconds wall clock time: 18 minutes 53.76 seconds (1133.76 seconds total)