Starting phenix.real_space_refine on Mon Feb 10 22:21:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jjo_36361/02_2025/8jjo_36361_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jjo_36361/02_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_36361/02_2025/8jjo_36361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jjo_36361/02_2025/8jjo_36361.map" model { file = "/net/cci-nas-00/data/ceres_data/8jjo_36361/02_2025/8jjo_36361_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jjo_36361/02_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-5592/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: 2.56, 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: 0.91 Conformation dependent library (CDL) restraints added in 378.8 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: 0.26 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: 0.77 Time building geometry restraints manager: 0.94 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: 0.430 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.230 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.930 ------------------------------------------------------------------------------- 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 : 0.346 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: 0.1130 time to fit residues: 7.8592 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 : 0.315 ------------------------------------------------------------------------------- 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 = 0.4569 r_free = 0.4569 target = 0.214369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.169475 restraints weight = 3468.417| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.61 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: 0.6973 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 : 0.314 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.1011 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 : 0.354 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.205400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.163114 restraints weight = 3313.361| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.26 r_work: 0.3996 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3083 Z= 0.194 Angle : 0.507 6.626 4184 Z= 0.270 Chirality : 0.039 0.116 488 Planarity : 0.003 0.028 513 Dihedral : 8.479 112.419 409 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.10 % Allowed : 19.50 % 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: 0.64 (0.45), residues: 371 helix: 1.26 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -3.38 (0.61), residues: 69 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 0.012 0.002 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 66 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.336 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.0963 time to fit residues: 8.1559 Evaluate side-chains 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.205049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.162775 restraints weight = 3436.006| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.28 r_work: 0.3977 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3083 Z= 0.214 Angle : 0.532 9.713 4184 Z= 0.274 Chirality : 0.039 0.111 488 Planarity : 0.003 0.028 513 Dihedral : 8.327 108.661 409 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.41 % Allowed : 21.98 % 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: 0.65 (0.45), residues: 371 helix: 1.26 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -3.42 (0.62), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 237 HIS 0.003 0.001 HIS F 178 PHE 0.009 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: 11 poor density : 53 time to evaluate : 0.359 Fit side-chains REVERT: F 220 SER cc_start: 0.7702 (m) cc_final: 0.7404 (t) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.0994 time to fit residues: 8.3661 Evaluate side-chains 62 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 341 THR Chi-restraints excluded: chain F residue 363 HIS 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: 0.8980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 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 = 0.4574 r_free = 0.4574 target = 0.214146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.168268 restraints weight = 3487.392| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.44 r_work: 0.3974 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1710 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= 0.193 Angle : 0.508 8.969 4184 Z= 0.265 Chirality : 0.038 0.112 488 Planarity : 0.003 0.028 513 Dihedral : 8.237 105.776 409 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.41 % Allowed : 22.91 % Favored : 73.68 % 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: 0.62 (0.46), residues: 371 helix: 1.26 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.66 (0.58), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 237 HIS 0.006 0.001 HIS F 363 PHE 0.008 0.001 PHE F 49 TYR 0.019 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 67 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.355 Fit side-chains REVERT: F 220 SER cc_start: 0.7643 (m) cc_final: 0.7345 (t) REVERT: F 373 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7089 (mm-30) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.1042 time to fit residues: 9.0050 Evaluate side-chains 62 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 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 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 374 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 15 optimal weight: 0.0870 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.4597 r_free = 0.4597 target = 0.216807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.174302 restraints weight = 3553.879| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.78 r_work: 0.4013 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3083 Z= 0.147 Angle : 0.485 9.000 4184 Z= 0.254 Chirality : 0.037 0.112 488 Planarity : 0.003 0.029 513 Dihedral : 8.100 99.969 409 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.10 % Allowed : 24.46 % 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: 0.89 (0.46), residues: 371 helix: 1.45 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.65 (0.56), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 237 HIS 0.003 0.001 HIS F 178 PHE 0.008 0.001 PHE F 49 TYR 0.019 0.002 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: 10 poor density : 55 time to evaluate : 0.292 Fit side-chains REVERT: F 236 ASN cc_start: 0.7989 (t0) cc_final: 0.7519 (t0) REVERT: F 245 LYS cc_start: 0.7847 (ttpp) cc_final: 0.7057 (tppt) outliers start: 10 outliers final: 9 residues processed: 60 average time/residue: 0.1029 time to fit residues: 8.0945 Evaluate side-chains 59 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 368 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.215906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.171780 restraints weight = 3502.860| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 2.74 r_work: 0.3999 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2161 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= 0.170 Angle : 0.514 10.394 4184 Z= 0.263 Chirality : 0.038 0.158 488 Planarity : 0.003 0.029 513 Dihedral : 8.184 97.204 409 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.02 % Allowed : 24.77 % 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: 0.75 (0.46), residues: 371 helix: 1.35 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.63 (0.58), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.001 0.000 HIS F 178 PHE 0.009 0.001 PHE F 49 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 68 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.342 Fit side-chains REVERT: F 236 ASN cc_start: 0.8214 (t0) cc_final: 0.7718 (t0) REVERT: F 245 LYS cc_start: 0.7777 (ttpp) cc_final: 0.7034 (tppt) outliers start: 13 outliers final: 11 residues processed: 63 average time/residue: 0.1209 time to fit residues: 9.7155 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 : 0.307 ------------------------------------------------------------------------------- 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 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 244 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 368 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.0270 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.4600 r_free = 0.4600 target = 0.217947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.172707 restraints weight = 3471.861| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.48 r_work: 0.4038 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3083 Z= 0.151 Angle : 0.510 10.216 4184 Z= 0.260 Chirality : 0.038 0.149 488 Planarity : 0.003 0.030 513 Dihedral : 7.767 93.593 409 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.48 % Allowed : 26.32 % 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: 0.82 (0.46), residues: 371 helix: 1.44 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.75 (0.55), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.001 0.000 HIS F 178 PHE 0.009 0.001 PHE F 49 TYR 0.017 0.001 TYR F 174 ARG 0.005 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 61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.253 Fit side-chains REVERT: F 236 ASN cc_start: 0.8171 (t0) cc_final: 0.7694 (t0) REVERT: F 245 LYS cc_start: 0.7754 (ttpp) cc_final: 0.7013 (tppt) outliers start: 8 outliers final: 7 residues processed: 58 average time/residue: 0.1068 time to fit residues: 8.1729 Evaluate side-chains 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 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: 0.0050 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 0.0050 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- 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 = 0.4610 r_free = 0.4610 target = 0.218983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.174913 restraints weight = 3473.259| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 3.03 r_work: 0.3999 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2403 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= 0.148 Angle : 0.504 9.635 4184 Z= 0.257 Chirality : 0.038 0.136 488 Planarity : 0.003 0.030 513 Dihedral : 7.469 91.317 409 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.79 % Allowed : 26.32 % 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: 1.09 (0.46), residues: 371 helix: 1.68 (0.31), residues: 298 sheet: None (None), residues: 0 loop : -3.48 (0.56), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 380 HIS 0.001 0.001 HIS F 286 PHE 0.011 0.001 PHE F 49 TYR 0.017 0.001 TYR F 174 ARG 0.004 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 63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.337 Fit side-chains REVERT: F 79 ASP cc_start: 0.7281 (m-30) cc_final: 0.7034 (t70) REVERT: F 236 ASN cc_start: 0.8157 (t0) cc_final: 0.7749 (t0) REVERT: F 245 LYS cc_start: 0.7756 (ttpp) cc_final: 0.7017 (tppt) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.1077 time to fit residues: 8.4538 Evaluate side-chains 60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.4860 ------------------------------------------------------------------------------- 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 = 0.4615 r_free = 0.4615 target = 0.219202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.174817 restraints weight = 3393.848| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 3.00 r_work: 0.4016 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 3083 Z= 0.163 Angle : 0.538 10.053 4184 Z= 0.274 Chirality : 0.039 0.175 488 Planarity : 0.003 0.032 513 Dihedral : 7.483 91.431 409 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.79 % Allowed : 26.63 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.45), residues: 371 helix: 1.70 (0.31), residues: 297 sheet: None (None), residues: 0 loop : -3.46 (0.55), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.001 0.000 HIS F 286 PHE 0.011 0.001 PHE F 49 TYR 0.016 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: 9 poor density : 51 time to evaluate : 0.474 Fit side-chains REVERT: F 79 ASP cc_start: 0.7304 (m-30) cc_final: 0.7030 (t70) REVERT: F 236 ASN cc_start: 0.8130 (t0) cc_final: 0.7694 (t0) REVERT: F 245 LYS cc_start: 0.7773 (ttpp) cc_final: 0.7041 (tppt) outliers start: 9 outliers final: 9 residues processed: 57 average time/residue: 0.1243 time to fit residues: 9.1086 Evaluate side-chains 60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- 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 = 0.4574 r_free = 0.4574 target = 0.209863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.168149 restraints weight = 3350.578| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.25 r_work: 0.4049 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3083 Z= 0.180 Angle : 0.559 8.397 4184 Z= 0.286 Chirality : 0.039 0.174 488 Planarity : 0.003 0.030 513 Dihedral : 7.518 91.875 409 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.79 % Allowed : 26.63 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.45), residues: 371 helix: 1.64 (0.31), residues: 297 sheet: None (None), residues: 0 loop : -3.41 (0.55), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.001 0.000 HIS F 178 PHE 0.010 0.001 PHE F 49 TYR 0.015 0.001 TYR F 174 ARG 0.003 0.000 ARG F 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.68 seconds wall clock time: 30 minutes 58.20 seconds (1858.20 seconds total)