Starting phenix.real_space_refine on Wed Mar 5 17:19:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jjo_36361/03_2025/8jjo_36361_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jjo_36361/03_2025/8jjo_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/cci-nas-00/data/ceres_data/8jjo_36361/03_2025/8jjo_36361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jjo_36361/03_2025/8jjo_36361.map" model { file = "/net/cci-nas-00/data/ceres_data/8jjo_36361/03_2025/8jjo_36361_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jjo_36361/03_2025/8jjo_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-5624/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: 2.29, per 1000 atoms: 0.76 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: 0.76 Conformation dependent library (CDL) restraints added in 349.3 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: 0.27 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: 0.73 Time building geometry restraints manager: 0.87 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: 0.420 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: 0.020 Process input model: 11.630 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- 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 : 0.327 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: 0.1115 time to fit residues: 7.7463 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 : 0.301 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.214366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.169376 restraints weight = 3470.212| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.62 r_work: 0.3980 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1057 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= 0.201 Angle : 0.529 5.780 4184 Z= 0.282 Chirality : 0.039 0.127 488 Planarity : 0.003 0.027 513 Dihedral : 8.791 121.330 409 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.10 % Allowed : 16.72 % Favored : 80.19 % 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 (0.63), 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 0.003 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 : 0.314 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.1056 time to fit residues: 8.9675 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 : 0.335 ------------------------------------------------------------------------------- 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 0 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.205069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.162919 restraints weight = 3314.693| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.24 r_work: 0.3991 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3083 Z= 0.201 Angle : 0.512 7.504 4184 Z= 0.271 Chirality : 0.039 0.115 488 Planarity : 0.003 0.028 513 Dihedral : 8.508 112.718 409 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.10 % Allowed : 19.81 % Favored : 77.09 % 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: 0.63 (0.45), residues: 371 helix: 1.25 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -3.38 (0.62), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 67 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.323 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.0949 time to fit residues: 8.1553 Evaluate side-chains 57 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 363 HIS ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.206759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.164246 restraints weight = 3419.806| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.29 r_work: 0.4003 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3083 Z= 0.188 Angle : 0.519 9.593 4184 Z= 0.267 Chirality : 0.038 0.115 488 Planarity : 0.003 0.028 513 Dihedral : 8.278 107.802 409 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.10 % Allowed : 22.29 % Favored : 74.61 % 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: 0.63 (0.45), residues: 371 helix: 1.28 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.72 (0.57), residues: 67 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 63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.296 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.0954 time to fit residues: 7.8350 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 : 0.326 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.208875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.166604 restraints weight = 3389.512| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.28 r_work: 0.4027 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3083 Z= 0.163 Angle : 0.489 8.927 4184 Z= 0.256 Chirality : 0.037 0.115 488 Planarity : 0.003 0.029 513 Dihedral : 8.032 103.986 409 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.10 % Allowed : 22.91 % Favored : 73.99 % 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: 1.37 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.66 (0.57), 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 0.009 0.001 PHE F 49 TYR 0.021 0.002 TYR F 174 ARG 0.002 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 64 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.307 Fit side-chains REVERT: F 236 ASN cc_start: 0.8022 (t0) cc_final: 0.7787 (t0) outliers start: 10 outliers final: 8 residues processed: 61 average time/residue: 0.0954 time to fit residues: 7.8317 Evaluate side-chains 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 197 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 341 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.0470 chunk 27 optimal weight: 0.0050 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.4892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.216705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.172918 restraints weight = 3562.463| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.67 r_work: 0.4024 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3083 Z= 0.149 Angle : 0.482 8.811 4184 Z= 0.252 Chirality : 0.037 0.143 488 Planarity : 0.003 0.029 513 Dihedral : 7.944 101.259 409 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.02 % Allowed : 23.84 % 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: 0.84 (0.46), residues: 371 helix: 1.41 (0.32), residues: 305 sheet: None (None), residues: 0 loop : -3.60 (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 0.007 0.001 PHE F 49 TYR 0.018 0.001 TYR F 174 ARG 0.002 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 65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.293 Fit side-chains REVERT: F 79 ASP cc_start: 0.7422 (m-30) cc_final: 0.7099 (t70) REVERT: F 236 ASN cc_start: 0.8211 (t0) cc_final: 0.7689 (t0) outliers start: 13 outliers final: 11 residues processed: 60 average time/residue: 0.0927 time to fit residues: 7.5262 Evaluate side-chains 61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 155 LEU Chi-restraints excluded: chain F residue 197 GLN 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 368 ASN 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 9 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.216769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.173143 restraints weight = 3496.374| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.66 r_work: 0.4015 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3083 Z= 0.163 Angle : 0.502 10.001 4184 Z= 0.258 Chirality : 0.038 0.141 488 Planarity : 0.003 0.029 513 Dihedral : 7.977 100.021 409 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.02 % Allowed : 23.84 % 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: 0.81 (0.46), residues: 371 helix: 1.39 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.61 (0.57), residues: 66 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 0.008 0.001 PHE F 49 TYR 0.017 0.001 TYR F 174 ARG 0.002 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 65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.331 Fit side-chains REVERT: F 79 ASP cc_start: 0.7413 (m-30) cc_final: 0.7090 (t0) REVERT: F 236 ASN cc_start: 0.8193 (t0) cc_final: 0.7729 (t0) REVERT: F 245 LYS cc_start: 0.7775 (ttpp) cc_final: 0.7017 (tppt) outliers start: 13 outliers final: 12 residues processed: 60 average time/residue: 0.1316 time to fit residues: 10.4884 Evaluate side-chains 62 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 197 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 341 THR Chi-restraints excluded: chain F residue 368 ASN 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 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.207635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.165628 restraints weight = 3392.469| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 2.28 r_work: 0.4027 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2124 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= 0.195 Angle : 0.522 10.915 4184 Z= 0.265 Chirality : 0.038 0.130 488 Planarity : 0.003 0.029 513 Dihedral : 8.180 99.593 409 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.56 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: 1.31 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.47 (0.58), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 237 HIS 0.001 0.000 HIS F 286 PHE 0.010 0.001 PHE F 49 TYR 0.015 0.002 TYR F 174 ARG 0.002 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 66 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.305 Fit side-chains REVERT: F 79 ASP cc_start: 0.7490 (m-30) cc_final: 0.7127 (t0) REVERT: F 236 ASN cc_start: 0.8208 (t0) cc_final: 0.7739 (t0) outliers start: 12 outliers final: 11 residues processed: 62 average time/residue: 0.0949 time to fit residues: 7.9032 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 : 0.306 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 0.0050 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.210382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.168605 restraints weight = 3376.114| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.28 r_work: 0.4055 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3083 Z= 0.158 Angle : 0.512 10.366 4184 Z= 0.260 Chirality : 0.038 0.121 488 Planarity : 0.003 0.030 513 Dihedral : 7.766 94.385 409 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.41 % Allowed : 24.15 % 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: 0.87 (0.46), residues: 371 helix: 1.45 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.62 (0.57), residues: 67 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 0.012 0.001 PHE F 49 TYR 0.016 0.001 TYR F 174 ARG 0.000 0.000 ARG F 371 *********************** 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 64 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.339 Fit side-chains REVERT: F 79 ASP cc_start: 0.7407 (m-30) cc_final: 0.7097 (t0) REVERT: F 236 ASN cc_start: 0.8150 (t0) cc_final: 0.7747 (t0) REVERT: F 245 LYS cc_start: 0.7729 (ttpp) cc_final: 0.6990 (tppt) REVERT: F 248 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7782 (mm-30) outliers start: 11 outliers final: 11 residues processed: 61 average time/residue: 0.1077 time to fit residues: 8.6684 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 : 0.334 ------------------------------------------------------------------------------- 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 197 GLN 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 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 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.211314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.165946 restraints weight = 3437.715| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.38 r_work: 0.3961 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3083 Z= 0.282 Angle : 0.601 13.335 4184 Z= 0.303 Chirality : 0.041 0.182 488 Planarity : 0.003 0.027 513 Dihedral : 7.720 95.510 409 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.41 % Allowed : 25.39 % Favored : 71.21 % 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: 0.80 (0.45), residues: 371 helix: 1.41 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -2.85 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 237 HIS 0.001 0.001 HIS F 172 PHE 0.012 0.001 PHE F 288 TYR 0.016 0.002 TYR F 383 ARG 0.002 0.000 ARG F 175 ********************** 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 65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.298 Fit side-chains REVERT: F 236 ASN cc_start: 0.8153 (t0) cc_final: 0.7764 (t0) REVERT: F 245 LYS cc_start: 0.7834 (ttpp) cc_final: 0.6948 (tppt) REVERT: F 286 HIS cc_start: 0.7244 (m-70) cc_final: 0.6974 (m-70) outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.1111 time to fit residues: 9.0567 Evaluate side-chains 59 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4584 r_free = 0.4584 target = 0.215377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169424 restraints weight = 3447.893| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.44 r_work: 0.4000 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3083 Z= 0.173 Angle : 0.561 11.798 4184 Z= 0.280 Chirality : 0.039 0.162 488 Planarity : 0.003 0.029 513 Dihedral : 7.615 94.596 409 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.10 % Allowed : 26.01 % Favored : 70.90 % 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: 0.94 (0.45), residues: 371 helix: 1.55 (0.31), residues: 292 sheet: None (None), residues: 0 loop : -3.03 (0.56), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 173 HIS 0.001 0.000 HIS F 286 PHE 0.011 0.001 PHE F 49 TYR 0.016 0.002 TYR F 174 ARG 0.001 0.000 ARG F 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.11 seconds wall clock time: 30 minutes 38.37 seconds (1838.37 seconds total)