Starting phenix.real_space_refine on Wed Jul 1 22:50:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jj8_36342/07_2026/8jj8_36342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jj8_36342/07_2026/8jj8_36342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8jj8_36342/07_2026/8jj8_36342.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jj8_36342/07_2026/8jj8_36342.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jj8_36342/07_2026/8jj8_36342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jj8_36342/07_2026/8jj8_36342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jj8_36342/07_2026/8jj8_36342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jj8_36342/07_2026/8jj8_36342.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 707 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 1984 2.51 5 N 488 2.21 5 O 531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3023 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2998 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 8, 'TRANS': 366} Chain breaks: 1 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H98': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.55, per 1000 atoms: 0.18 Number of scatterers: 3023 At special positions: 0 Unit cell: (57.78, 103.79, 82.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 531 8.00 N 488 7.00 C 1984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 106 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.19 Conformation dependent library (CDL) restraints added in 63.8 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: 17 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'F' and resid 30 through 56 removed outlier: 4.023A pdb=" N MET F 36 " --> pdb=" O TRP F 32 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 93 removed outlier: 3.531A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL F 87 " --> pdb=" O GLY F 83 " (cutoff:3.500A) Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 102 through 136 Processing helix chain 'F' and resid 137 through 143 removed outlier: 4.230A pdb=" N SER F 143 " --> pdb=" O PHE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 Processing helix chain 'F' and resid 166 through 171 removed outlier: 4.261A pdb=" N MET F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 186 removed outlier: 3.780A pdb=" N ASN F 183 " --> pdb=" O GLN F 179 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 208 Processing helix chain 'F' and resid 208 through 249 removed outlier: 3.608A pdb=" N LYS F 249 " --> pdb=" O LYS F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 273 removed outlier: 3.682A pdb=" N VAL F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 305 Processing helix chain 'F' and resid 306 through 365 removed outlier: 4.741A pdb=" N GLN F 326 " --> pdb=" O ASN F 322 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU F 329 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Proline residue: F 355 - end of helix removed outlier: 3.920A pdb=" N ILE F 361 " --> pdb=" O PHE F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 370 removed outlier: 3.517A pdb=" N ILE F 370 " --> pdb=" O ASP F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 384 Processing helix chain 'F' and resid 384 through 389 removed outlier: 3.606A pdb=" N PHE F 388 " --> pdb=" O VAL F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 396 through 407 removed outlier: 3.590A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 738 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: 0.26 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 478 1.29 - 1.42: 820 1.42 - 1.55: 1760 1.55 - 1.68: 2 1.68 - 1.81: 31 Bond restraints: 3091 Sorted by residual: bond pdb=" C TYR F 328 " pdb=" O TYR F 328 " ideal model delta sigma weight residual 1.236 1.161 0.076 1.26e-02 6.30e+03 3.61e+01 bond pdb=" C LYS F 327 " pdb=" O LYS F 327 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.16e-02 7.43e+03 1.61e+01 bond pdb=" C GLN F 326 " pdb=" O GLN F 326 " ideal model delta sigma weight residual 1.235 1.286 -0.050 1.26e-02 6.30e+03 1.60e+01 bond pdb=" C LEU F 342 " pdb=" O LEU F 342 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.26e-02 6.30e+03 1.27e+01 bond pdb=" C ALA F 338 " pdb=" O ALA F 338 " ideal model delta sigma weight residual 1.236 1.281 -0.045 1.29e-02 6.01e+03 1.22e+01 ... (remaining 3086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 4144 3.48 - 6.97: 46 6.97 - 10.45: 5 10.45 - 13.93: 0 13.93 - 17.42: 1 Bond angle restraints: 4196 Sorted by residual: angle pdb=" O ILE F 325 " pdb=" C ILE F 325 " pdb=" N GLN F 326 " ideal model delta sigma weight residual 121.96 130.61 -8.65 8.40e-01 1.42e+00 1.06e+02 angle pdb=" CA ILE F 325 " pdb=" C ILE F 325 " pdb=" N GLN F 326 " ideal model delta sigma weight residual 115.25 106.83 8.42 9.50e-01 1.11e+00 7.85e+01 angle pdb=" N LYS F 340 " pdb=" CA LYS F 340 " pdb=" C LYS F 340 " ideal model delta sigma weight residual 111.28 102.34 8.94 1.09e+00 8.42e-01 6.73e+01 angle pdb=" N GLN F 326 " pdb=" CA GLN F 326 " pdb=" C GLN F 326 " ideal model delta sigma weight residual 110.80 93.38 17.42 2.13e+00 2.20e-01 6.69e+01 angle pdb=" N LEU F 329 " pdb=" CA LEU F 329 " pdb=" C LEU F 329 " ideal model delta sigma weight residual 111.07 103.97 7.10 1.07e+00 8.73e-01 4.41e+01 ... (remaining 4191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1615 17.82 - 35.64: 164 35.64 - 53.46: 28 53.46 - 71.28: 4 71.28 - 89.10: 3 Dihedral angle restraints: 1814 sinusoidal: 706 harmonic: 1108 Sorted by residual: dihedral pdb=" CB CYS F 106 " pdb=" SG CYS F 106 " pdb=" SG CYS F 191 " pdb=" CB CYS F 191 " ideal model delta sinusoidal sigma weight residual -86.00 -175.10 89.10 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CA MET F 96 " pdb=" C MET F 96 " pdb=" N LYS F 97 " pdb=" CA LYS F 97 " ideal model delta harmonic sigma weight residual 180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" N GLN F 326 " pdb=" C GLN F 326 " pdb=" CA GLN F 326 " pdb=" CB GLN F 326 " ideal model delta harmonic sigma weight residual 122.80 114.83 7.97 0 2.50e+00 1.60e-01 1.02e+01 ... (remaining 1811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 399 0.060 - 0.120: 80 0.120 - 0.180: 6 0.180 - 0.240: 2 0.240 - 0.300: 2 Chirality restraints: 489 Sorted by residual: chirality pdb=" CA GLN F 326 " pdb=" N GLN F 326 " pdb=" C GLN F 326 " pdb=" CB GLN F 326 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LYS F 340 " pdb=" N LYS F 340 " pdb=" C LYS F 340 " pdb=" CB LYS F 340 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA LEU F 339 " pdb=" N LEU F 339 " pdb=" C LEU F 339 " pdb=" CB LEU F 339 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 486 not shown) Planarity restraints: 515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 326 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLN F 326 " -0.073 2.00e-02 2.50e+03 pdb=" O GLN F 326 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS F 327 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 329 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU F 329 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU F 329 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS F 330 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 236 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C ASN F 236 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN F 236 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP F 237 " 0.016 2.00e-02 2.50e+03 ... (remaining 512 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 57 2.67 - 3.22: 3111 3.22 - 3.78: 4782 3.78 - 4.34: 6157 4.34 - 4.90: 10166 Nonbonded interactions: 24273 Sorted by model distance: nonbonded pdb=" OE2 GLU F 187 " pdb=" OG1 THR F 189 " model vdw 2.107 3.040 nonbonded pdb=" OG SER F 203 " pdb=" O2 H98 F 501 " model vdw 2.191 3.040 nonbonded pdb=" O THR F 341 " pdb=" C LEU F 342 " model vdw 2.229 3.270 nonbonded pdb=" O THR F 239 " pdb=" ND2 ASN F 243 " model vdw 2.315 3.120 nonbonded pdb=" OD2 ASP F 113 " pdb=" OH TYR F 383 " model vdw 2.323 3.040 ... (remaining 24268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.900 Find NCS groups from input model: 0.000 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:0.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 3093 Z= 0.351 Angle : 0.898 17.416 4200 Z= 0.611 Chirality : 0.050 0.300 489 Planarity : 0.005 0.042 515 Dihedral : 14.290 74.011 1086 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.86 % Allowed : 1.55 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.45), residues: 371 helix: 1.06 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -3.25 (0.85), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 400 TYR 0.020 0.002 TYR F 328 PHE 0.021 0.002 PHE F 284 TRP 0.011 0.001 TRP F 237 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.35 ( 3091) covalent geometry : angle 0.89806 / 0.61 ( 4196) SS BOND : bond 0.00176 / 0.09 ( 2) SS BOND : angle 0.50549 / 0.23 ( 4) hydrogen bonds : bond 0.13688 / 8.01 ( 247) hydrogen bonds : angle 5.56686 / 3.92 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.066 Fit side-chains REVERT: F 230 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7669 (tp) REVERT: F 269 ASP cc_start: 0.7007 (m-30) cc_final: 0.6791 (m-30) REVERT: F 331 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6948 (t80) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.0386 time to fit residues: 3.8100 Evaluate side-chains 63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 331 PHE Chi-restraints excluded: chain F residue 332 CYS Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 379 ASN F 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.188802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147684 restraints weight = 3697.506| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.65 r_work: 0.3589 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3093 Z= 0.168 Angle : 0.621 5.823 4200 Z= 0.332 Chirality : 0.042 0.165 489 Planarity : 0.003 0.024 515 Dihedral : 6.473 54.023 410 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.86 % Allowed : 7.12 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.44), residues: 371 helix: 1.46 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -3.70 (0.69), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 400 TYR 0.017 0.002 TYR F 328 PHE 0.015 0.002 PHE F 284 TRP 0.017 0.001 TRP F 237 HIS 0.002 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 3091) covalent geometry : angle 0.62143 / 0.33 ( 4196) SS BOND : bond 0.00181 / 0.09 ( 2) SS BOND : angle 0.52200 / 0.29 ( 4) hydrogen bonds : bond 0.05590 / 3.73 ( 247) hydrogen bonds : angle 4.25901 / 3.07 ( 738) *********************** 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 68 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.100 Fit side-chains REVERT: F 122 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7997 (mm-30) REVERT: F 230 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6871 (tp) REVERT: F 269 ASP cc_start: 0.7970 (m-30) cc_final: 0.7608 (m-30) REVERT: F 326 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7995 (mm-40) outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 0.0319 time to fit residues: 2.8879 Evaluate side-chains 54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.190246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150269 restraints weight = 3735.305| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.56 r_work: 0.3619 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3093 Z= 0.142 Angle : 0.579 7.043 4200 Z= 0.307 Chirality : 0.040 0.148 489 Planarity : 0.003 0.023 515 Dihedral : 5.845 54.901 403 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.79 % Allowed : 10.22 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.44), residues: 371 helix: 1.70 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -3.66 (0.68), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 400 TYR 0.023 0.002 TYR F 324 PHE 0.015 0.001 PHE F 284 TRP 0.026 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 3091) covalent geometry : angle 0.57927 / 0.31 ( 4196) SS BOND : bond 0.00233 / 0.12 ( 2) SS BOND : angle 0.67461 / 0.36 ( 4) hydrogen bonds : bond 0.04964 / 3.33 ( 247) hydrogen bonds : angle 4.12052 / 2.97 ( 738) *********************** 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 63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.088 Fit side-chains REVERT: F 122 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7987 (mm-30) REVERT: F 230 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6907 (tp) REVERT: F 269 ASP cc_start: 0.7974 (m-30) cc_final: 0.7604 (m-30) REVERT: F 326 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7844 (mm-40) outliers start: 9 outliers final: 3 residues processed: 60 average time/residue: 0.0332 time to fit residues: 2.7496 Evaluate side-chains 55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 341 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.192096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152023 restraints weight = 3723.515| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.57 r_work: 0.3632 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3093 Z= 0.134 Angle : 0.554 6.582 4200 Z= 0.296 Chirality : 0.039 0.122 489 Planarity : 0.003 0.021 515 Dihedral : 5.797 56.615 403 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.17 % Allowed : 12.07 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.45), residues: 371 helix: 1.83 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -3.61 (0.70), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 400 TYR 0.015 0.002 TYR F 324 PHE 0.014 0.001 PHE F 284 TRP 0.024 0.001 TRP F 237 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 3091) covalent geometry : angle 0.55429 / 0.30 ( 4196) SS BOND : bond 0.00229 / 0.12 ( 2) SS BOND : angle 0.61182 / 0.33 ( 4) hydrogen bonds : bond 0.04725 / 3.21 ( 247) hydrogen bonds : angle 4.07951 / 2.94 ( 738) *********************** 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 61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.121 Fit side-chains REVERT: F 243 ASN cc_start: 0.8296 (m-40) cc_final: 0.8039 (m110) REVERT: F 326 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7819 (mm-40) REVERT: F 360 ASN cc_start: 0.8040 (t0) cc_final: 0.7702 (m-40) outliers start: 7 outliers final: 4 residues processed: 57 average time/residue: 0.0261 time to fit residues: 2.0892 Evaluate side-chains 55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.190734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154031 restraints weight = 3721.266| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.47 r_work: 0.3609 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 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 : 0.003 0.030 3093 Z= 0.145 Angle : 0.558 7.004 4200 Z= 0.297 Chirality : 0.039 0.115 489 Planarity : 0.003 0.021 515 Dihedral : 4.973 33.918 400 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.17 % Allowed : 14.55 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.45), residues: 371 helix: 1.84 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -3.56 (0.69), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 400 TYR 0.017 0.002 TYR F 324 PHE 0.013 0.001 PHE F 284 TRP 0.025 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 3091) covalent geometry : angle 0.55771 / 0.30 ( 4196) SS BOND : bond 0.00214 / 0.11 ( 2) SS BOND : angle 0.60138 / 0.37 ( 4) hydrogen bonds : bond 0.04750 / 3.24 ( 247) hydrogen bonds : angle 4.04690 / 2.91 ( 738) *********************** 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 60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.067 Fit side-chains REVERT: F 243 ASN cc_start: 0.8188 (m-40) cc_final: 0.7895 (m110) REVERT: F 326 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7926 (mm-40) REVERT: F 342 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.5666 (mp) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.0290 time to fit residues: 2.2212 Evaluate side-chains 61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.190226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149394 restraints weight = 3755.557| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.61 r_work: 0.3591 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3093 Z= 0.145 Angle : 0.558 7.201 4200 Z= 0.298 Chirality : 0.039 0.116 489 Planarity : 0.003 0.020 515 Dihedral : 4.960 34.126 400 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.17 % Allowed : 16.41 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.45), residues: 371 helix: 1.89 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -3.71 (0.67), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 400 TYR 0.022 0.002 TYR F 324 PHE 0.014 0.001 PHE F 284 TRP 0.025 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 3091) covalent geometry : angle 0.55781 / 0.30 ( 4196) SS BOND : bond 0.00240 / 0.13 ( 2) SS BOND : angle 0.62317 / 0.34 ( 4) hydrogen bonds : bond 0.04704 / 3.21 ( 247) hydrogen bonds : angle 4.04045 / 2.91 ( 738) *********************** 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 59 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.084 Fit side-chains REVERT: F 122 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7830 (mm-30) REVERT: F 243 ASN cc_start: 0.8184 (m-40) cc_final: 0.7731 (m110) REVERT: F 251 ASP cc_start: 0.7588 (t0) cc_final: 0.7294 (t0) REVERT: F 269 ASP cc_start: 0.7979 (m-30) cc_final: 0.7613 (m-30) REVERT: F 326 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7975 (mm-40) REVERT: F 342 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.5593 (mp) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 0.0349 time to fit residues: 2.7350 Evaluate side-chains 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.188736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148112 restraints weight = 3736.962| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.58 r_work: 0.3586 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3093 Z= 0.145 Angle : 0.568 7.927 4200 Z= 0.300 Chirality : 0.039 0.120 489 Planarity : 0.003 0.020 515 Dihedral : 4.996 34.171 400 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.17 % Allowed : 16.10 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.45), residues: 371 helix: 1.93 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.40 (0.73), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 400 TYR 0.024 0.002 TYR F 324 PHE 0.017 0.001 PHE F 284 TRP 0.034 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 3091) covalent geometry : angle 0.56817 / 0.30 ( 4196) SS BOND : bond 0.00208 / 0.11 ( 2) SS BOND : angle 0.81863 / 0.51 ( 4) hydrogen bonds : bond 0.04720 / 3.24 ( 247) hydrogen bonds : angle 4.01910 / 2.89 ( 738) *********************** 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 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.126 Fit side-chains REVERT: F 122 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7680 (mm-30) REVERT: F 243 ASN cc_start: 0.8161 (m-40) cc_final: 0.7829 (m110) REVERT: F 251 ASP cc_start: 0.7524 (t0) cc_final: 0.7237 (t0) REVERT: F 269 ASP cc_start: 0.7970 (m-30) cc_final: 0.7598 (m-30) REVERT: F 326 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7967 (mm-40) REVERT: F 342 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.5563 (mp) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.0291 time to fit residues: 2.1587 Evaluate side-chains 55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.189423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153040 restraints weight = 3821.097| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.48 r_work: 0.3593 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3093 Z= 0.147 Angle : 0.564 8.166 4200 Z= 0.299 Chirality : 0.039 0.124 489 Planarity : 0.003 0.019 515 Dihedral : 5.025 34.525 400 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.86 % Allowed : 17.03 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.45), residues: 371 helix: 1.94 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.27 (0.74), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 400 TYR 0.028 0.002 TYR F 324 PHE 0.018 0.001 PHE F 284 TRP 0.043 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 3091) covalent geometry : angle 0.56422 / 0.30 ( 4196) SS BOND : bond 0.00221 / 0.12 ( 2) SS BOND : angle 0.72957 / 0.45 ( 4) hydrogen bonds : bond 0.04717 / 3.23 ( 247) hydrogen bonds : angle 4.00328 / 2.88 ( 738) *********************** 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 57 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.098 Fit side-chains REVERT: F 99 TRP cc_start: 0.8140 (t-100) cc_final: 0.7849 (t-100) REVERT: F 101 PHE cc_start: 0.7813 (m-80) cc_final: 0.7608 (m-80) REVERT: F 243 ASN cc_start: 0.8121 (m-40) cc_final: 0.7780 (m110) REVERT: F 251 ASP cc_start: 0.7479 (t0) cc_final: 0.7248 (t0) REVERT: F 269 ASP cc_start: 0.7954 (m-30) cc_final: 0.7636 (m-30) REVERT: F 326 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7964 (mm-40) REVERT: F 342 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.5583 (mp) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.0348 time to fit residues: 2.6534 Evaluate side-chains 55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.188766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152469 restraints weight = 3855.883| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.46 r_work: 0.3587 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3093 Z= 0.152 Angle : 0.589 8.573 4200 Z= 0.306 Chirality : 0.039 0.130 489 Planarity : 0.003 0.019 515 Dihedral : 5.015 34.294 400 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.86 % Allowed : 17.34 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.45), residues: 371 helix: 1.91 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.18 (0.75), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 400 TYR 0.032 0.002 TYR F 324 PHE 0.019 0.001 PHE F 284 TRP 0.044 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3091) covalent geometry : angle 0.58898 / 0.31 ( 4196) SS BOND : bond 0.00223 / 0.12 ( 2) SS BOND : angle 0.62031 / 0.46 ( 4) hydrogen bonds : bond 0.04783 / 3.27 ( 247) hydrogen bonds : angle 4.01236 / 2.89 ( 738) *********************** 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 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.073 Fit side-chains REVERT: F 101 PHE cc_start: 0.7829 (m-80) cc_final: 0.7613 (m-80) REVERT: F 243 ASN cc_start: 0.8086 (m-40) cc_final: 0.7765 (m110) REVERT: F 251 ASP cc_start: 0.7538 (t0) cc_final: 0.7306 (t0) REVERT: F 269 ASP cc_start: 0.8012 (m-30) cc_final: 0.7659 (m-30) REVERT: F 326 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7954 (mm-40) REVERT: F 342 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.5638 (mp) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.0250 time to fit residues: 1.8633 Evaluate side-chains 52 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.189849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148992 restraints weight = 3776.056| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.62 r_work: 0.3587 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3093 Z= 0.141 Angle : 0.576 8.824 4200 Z= 0.301 Chirality : 0.039 0.126 489 Planarity : 0.003 0.025 515 Dihedral : 5.035 34.670 400 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.77 % Favored : 95.96 % Rotamer: Outliers : 1.86 % Allowed : 18.27 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.45), residues: 371 helix: 1.94 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.20 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 400 TYR 0.032 0.002 TYR F 324 PHE 0.019 0.001 PHE F 284 TRP 0.045 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 3091) covalent geometry : angle 0.57573 / 0.30 ( 4196) SS BOND : bond 0.00181 / 0.09 ( 2) SS BOND : angle 0.56988 / 0.38 ( 4) hydrogen bonds : bond 0.04674 / 3.20 ( 247) hydrogen bonds : angle 3.98923 / 2.88 ( 738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.065 Fit side-chains REVERT: F 243 ASN cc_start: 0.8128 (m-40) cc_final: 0.7796 (m110) REVERT: F 251 ASP cc_start: 0.7608 (t0) cc_final: 0.7350 (t0) REVERT: F 269 ASP cc_start: 0.7969 (m-30) cc_final: 0.7638 (m-30) REVERT: F 326 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7938 (mm-40) REVERT: F 342 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.5701 (mp) outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.0253 time to fit residues: 1.7185 Evaluate side-chains 50 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.189240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.148814 restraints weight = 3774.376| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.59 r_work: 0.3604 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3093 Z= 0.139 Angle : 0.574 8.626 4200 Z= 0.301 Chirality : 0.039 0.123 489 Planarity : 0.003 0.019 515 Dihedral : 5.020 34.498 400 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.04 % Favored : 95.69 % Rotamer: Outliers : 1.86 % Allowed : 18.89 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.45), residues: 371 helix: 1.94 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -3.12 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 400 TYR 0.032 0.002 TYR F 324 PHE 0.018 0.001 PHE F 284 TRP 0.039 0.002 TRP F 237 HIS 0.002 0.000 HIS F 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 3091) covalent geometry : angle 0.57440 / 0.30 ( 4196) SS BOND : bond 0.00113 / 0.06 ( 2) SS BOND : angle 0.44470 / 0.28 ( 4) hydrogen bonds : bond 0.04611 / 3.16 ( 247) hydrogen bonds : angle 4.00847 / 2.89 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 768.22 seconds wall clock time: 13 minutes 50.80 seconds (830.80 seconds total)