Starting phenix.real_space_refine on Tue Aug 4 14:09:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6p_50237/08_2026/9f6p_50237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6p_50237/08_2026/9f6p_50237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6p_50237/08_2026/9f6p_50237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6p_50237/08_2026/9f6p_50237.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6p_50237/08_2026/9f6p_50237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6p_50237/08_2026/9f6p_50237.cif" } resolution = 3.7 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= 0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 22 5.16 5 C 2460 2.51 5 N 606 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3720 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3719 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.17, per 1000 atoms: 0.31 Number of scatterers: 3720 At special positions: 0 Unit cell: (83.328, 69.006, 79.422, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 22 16.00 O 631 8.00 N 606 7.00 C 2460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 354 " 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: 0.38 Conformation dependent library (CDL) restraints added in 159.2 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 886 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.913A pdb=" N SER A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.918A pdb=" N ASP A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 118 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 130 through 164 removed outlier: 3.566A pdb=" N SER A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 188 removed outlier: 3.849A pdb=" N GLY A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 218 removed outlier: 3.627A pdb=" N ARG A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 237 through 252 removed outlier: 4.224A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 4.035A pdb=" N ILE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 311 removed outlier: 4.347A pdb=" N ILE A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 344 through 357 Processing helix chain 'A' and resid 357 through 391 removed outlier: 4.293A pdb=" N LEU A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 420 through 439 Processing helix chain 'A' and resid 439 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 462 through 488 Processing helix chain 'A' and resid 497 through 523 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.721A pdb=" N TYR A 537 " --> pdb=" O HIS A 533 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 906 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: 0.37 Time building geometry restraints manager: 0.49 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: 1151 1.34 - 1.46: 954 1.46 - 1.58: 1675 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 3814 Sorted by residual: bond pdb=" N MET A 253 " pdb=" CA MET A 253 " ideal model delta sigma weight residual 1.454 1.477 -0.023 1.30e-02 5.92e+03 3.21e+00 bond pdb=" N LEU A 437 " pdb=" CA LEU A 437 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.28e-02 6.10e+03 2.45e+00 bond pdb=" CA ARG A 218 " pdb=" CB ARG A 218 " ideal model delta sigma weight residual 1.522 1.532 -0.010 7.00e-03 2.04e+04 1.86e+00 bond pdb=" CB GLU A 268 " pdb=" CG GLU A 268 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB ARG A 193 " pdb=" CG ARG A 193 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 3809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 5013 2.10 - 4.19: 143 4.19 - 6.29: 31 6.29 - 8.39: 9 8.39 - 10.48: 6 Bond angle restraints: 5202 Sorted by residual: angle pdb=" N LEU A 437 " pdb=" CA LEU A 437 " pdb=" CB LEU A 437 " ideal model delta sigma weight residual 110.28 104.86 5.42 1.55e+00 4.16e-01 1.22e+01 angle pdb=" CB MET A 68 " pdb=" CG MET A 68 " pdb=" SD MET A 68 " ideal model delta sigma weight residual 112.70 123.09 -10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA GLN A 312 " pdb=" CB GLN A 312 " pdb=" CG GLN A 312 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA LYS A 91 " pdb=" CB LYS A 91 " pdb=" CG LYS A 91 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.60e+00 angle pdb=" CA LEU A 391 " pdb=" CB LEU A 391 " pdb=" CG LEU A 391 " ideal model delta sigma weight residual 116.30 126.78 -10.48 3.50e+00 8.16e-02 8.97e+00 ... (remaining 5197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 1790 15.84 - 31.68: 291 31.68 - 47.52: 90 47.52 - 63.36: 29 63.36 - 79.20: 4 Dihedral angle restraints: 2204 sinusoidal: 819 harmonic: 1385 Sorted by residual: dihedral pdb=" CB CYS A 322 " pdb=" SG CYS A 322 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -156.87 70.87 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CA ALA A 342 " pdb=" C ALA A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta harmonic sigma weight residual 180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TYR A 311 " pdb=" C TYR A 311 " pdb=" N GLN A 312 " pdb=" CA GLN A 312 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 2201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 509 0.062 - 0.124: 96 0.124 - 0.186: 8 0.186 - 0.247: 2 0.247 - 0.309: 1 Chirality restraints: 616 Sorted by residual: chirality pdb=" CG LEU A 102 " pdb=" CB LEU A 102 " pdb=" CD1 LEU A 102 " pdb=" CD2 LEU A 102 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB VAL A 174 " pdb=" CA VAL A 174 " pdb=" CG1 VAL A 174 " pdb=" CG2 VAL A 174 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR A 177 " pdb=" CA THR A 177 " pdb=" OG1 THR A 177 " pdb=" CG2 THR A 177 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 613 not shown) Planarity restraints: 643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 311 " -0.016 2.00e-02 2.50e+03 1.31e-02 3.43e+00 pdb=" CG TYR A 311 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 311 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 311 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 311 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 311 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 311 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 311 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 270 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" CG ASP A 270 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 270 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 270 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 230 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 231 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.022 5.00e-02 4.00e+02 ... (remaining 640 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 46 2.65 - 3.21: 3781 3.21 - 3.78: 6236 3.78 - 4.34: 7513 4.34 - 4.90: 12437 Nonbonded interactions: 30013 Sorted by model distance: nonbonded pdb=" OD1 ASN A 77 " pdb="MN MN A 701 " model vdw 2.090 2.320 nonbonded pdb=" O SER A 374 " pdb=" OG1 THR A 378 " model vdw 2.263 3.040 nonbonded pdb=" O LYS A 131 " pdb=" OG1 THR A 135 " model vdw 2.332 3.040 nonbonded pdb=" O CYS A 518 " pdb=" ND1 HIS A 522 " model vdw 2.341 3.120 nonbonded pdb=" OG SER A 451 " pdb=" OD1 ASN A 461 " model vdw 2.351 3.040 ... (remaining 30008 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 group one per residue 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.280 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 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 : 0.004 0.038 3816 Z= 0.186 Angle : 0.931 10.484 5206 Z= 0.455 Chirality : 0.048 0.309 616 Planarity : 0.005 0.040 643 Dihedral : 18.008 79.197 1312 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.05 % Allowed : 44.10 % Favored : 53.85 % 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: 1.39 (0.38), residues: 480 helix: 1.66 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -1.89 (0.59), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 400 TYR 0.029 0.002 TYR A 311 PHE 0.024 0.002 PHE A 184 TRP 0.020 0.002 TRP A 138 HIS 0.003 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 3814) covalent geometry : angle 0.92868 / 0.45 ( 5202) SS BOND : bond 0.00168 / 0.08 ( 2) SS BOND : angle 2.48456 / 0.79 ( 4) hydrogen bonds : bond 0.09532 / 6.06 ( 302) hydrogen bonds : angle 5.50313 / 3.96 ( 906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.2433 (OUTLIER) cc_final: 0.2194 (tp) REVERT: A 68 MET cc_start: 0.6634 (tpp) cc_final: 0.5464 (tpt) REVERT: A 135 THR cc_start: 0.9084 (m) cc_final: 0.8877 (t) REVERT: A 178 ILE cc_start: 0.8263 (tp) cc_final: 0.7995 (pt) REVERT: A 214 TYR cc_start: 0.7164 (t80) cc_final: 0.6904 (t80) REVERT: A 228 LEU cc_start: 0.8311 (tp) cc_final: 0.7999 (tt) REVERT: A 278 ARG cc_start: 0.7002 (tmt170) cc_final: 0.6615 (mtm-85) REVERT: A 287 GLU cc_start: 0.8032 (tt0) cc_final: 0.7327 (tm-30) REVERT: A 393 LEU cc_start: 0.8120 (tt) cc_final: 0.7906 (mt) REVERT: A 475 LEU cc_start: 0.8984 (tp) cc_final: 0.8659 (pp) REVERT: A 537 TYR cc_start: 0.8050 (m-10) cc_final: 0.7696 (m-10) outliers start: 8 outliers final: 4 residues processed: 153 average time/residue: 0.0439 time to fit residues: 8.7290 Evaluate side-chains 116 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.6333 > 50:) chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 461 ASN A 529 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.154070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134045 restraints weight = 7609.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137828 restraints weight = 4031.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140333 restraints weight = 2522.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142315 restraints weight = 1797.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.143614 restraints weight = 1383.374| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3816 Z= 0.154 Angle : 0.697 7.271 5206 Z= 0.347 Chirality : 0.041 0.136 616 Planarity : 0.005 0.041 643 Dihedral : 6.260 48.551 527 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.67 % Allowed : 35.90 % Favored : 57.44 % 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: 1.42 (0.38), residues: 480 helix: 1.72 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -2.03 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 400 TYR 0.013 0.001 TYR A 311 PHE 0.026 0.002 PHE A 72 TRP 0.017 0.001 TRP A 94 HIS 0.009 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 3814) covalent geometry : angle 0.69689 / 0.35 ( 5202) SS BOND : bond 0.00076 / 0.04 ( 2) SS BOND : angle 1.19103 / 0.39 ( 4) hydrogen bonds : bond 0.04219 / 2.69 ( 302) hydrogen bonds : angle 4.64396 / 3.34 ( 906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 66 PHE cc_start: 0.7687 (m-10) cc_final: 0.7427 (m-10) REVERT: A 67 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7091 (pp) REVERT: A 72 PHE cc_start: 0.7908 (m-80) cc_final: 0.7484 (m-80) REVERT: A 107 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8720 (mm-40) REVERT: A 178 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8172 (pt) REVERT: A 228 LEU cc_start: 0.8370 (tp) cc_final: 0.8018 (tt) REVERT: A 278 ARG cc_start: 0.7237 (tmt170) cc_final: 0.6897 (mtm-85) REVERT: A 287 GLU cc_start: 0.7965 (tt0) cc_final: 0.7675 (tm-30) REVERT: A 364 TRP cc_start: 0.8566 (OUTLIER) cc_final: 0.7232 (t-100) REVERT: A 378 THR cc_start: 0.9185 (m) cc_final: 0.8928 (p) REVERT: A 420 ASP cc_start: 0.7937 (m-30) cc_final: 0.7631 (m-30) REVERT: A 433 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7942 (p) REVERT: A 484 VAL cc_start: 0.7600 (t) cc_final: 0.7249 (p) REVERT: A 535 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7415 (m-80) outliers start: 26 outliers final: 9 residues processed: 136 average time/residue: 0.0383 time to fit residues: 7.0529 Evaluate side-chains 126 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 535 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 39 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133018 restraints weight = 7681.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136736 restraints weight = 4155.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139334 restraints weight = 2644.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141225 restraints weight = 1893.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142399 restraints weight = 1473.765| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3816 Z= 0.143 Angle : 0.667 8.187 5206 Z= 0.327 Chirality : 0.040 0.226 616 Planarity : 0.005 0.041 643 Dihedral : 5.453 49.838 522 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 8.72 % Allowed : 31.28 % Favored : 60.00 % 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: 1.36 (0.38), residues: 480 helix: 1.64 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.05 (0.57), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.016 0.001 TYR A 214 PHE 0.027 0.001 PHE A 483 TRP 0.013 0.001 TRP A 94 HIS 0.008 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 3814) covalent geometry : angle 0.66649 / 0.33 ( 5202) SS BOND : bond 0.00097 / 0.05 ( 2) SS BOND : angle 1.05698 / 0.34 ( 4) hydrogen bonds : bond 0.03962 / 2.56 ( 302) hydrogen bonds : angle 4.51031 / 3.27 ( 906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7095 (pp) REVERT: A 68 MET cc_start: 0.5983 (tpt) cc_final: 0.5771 (tpt) REVERT: A 91 LYS cc_start: 0.8722 (mmtt) cc_final: 0.7613 (mtmt) REVERT: A 178 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8163 (pt) REVERT: A 195 LEU cc_start: 0.7389 (tp) cc_final: 0.6932 (tt) REVERT: A 228 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 276 ASP cc_start: 0.7327 (m-30) cc_final: 0.6900 (m-30) REVERT: A 278 ARG cc_start: 0.7195 (tmt170) cc_final: 0.6872 (mtm-85) REVERT: A 364 TRP cc_start: 0.8583 (OUTLIER) cc_final: 0.7058 (t-100) REVERT: A 423 ASP cc_start: 0.8132 (m-30) cc_final: 0.7917 (m-30) REVERT: A 433 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 466 LYS cc_start: 0.7782 (mttm) cc_final: 0.7374 (mttm) REVERT: A 484 VAL cc_start: 0.7553 (t) cc_final: 0.7250 (p) outliers start: 34 outliers final: 17 residues processed: 135 average time/residue: 0.0331 time to fit residues: 5.8091 Evaluate side-chains 130 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.0670 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132419 restraints weight = 7563.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136060 restraints weight = 4077.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138640 restraints weight = 2579.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140363 restraints weight = 1839.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.141531 restraints weight = 1440.838| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3816 Z= 0.141 Angle : 0.658 10.728 5206 Z= 0.320 Chirality : 0.039 0.135 616 Planarity : 0.005 0.039 643 Dihedral : 5.163 51.616 522 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 9.49 % Allowed : 31.28 % Favored : 59.23 % 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: 1.44 (0.38), residues: 480 helix: 1.72 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.14 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.013 0.001 TYR A 214 PHE 0.018 0.001 PHE A 72 TRP 0.013 0.001 TRP A 94 HIS 0.006 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 3814) covalent geometry : angle 0.65793 / 0.32 ( 5202) SS BOND : bond 0.00133 / 0.07 ( 2) SS BOND : angle 1.00100 / 0.33 ( 4) hydrogen bonds : bond 0.03828 / 2.47 ( 302) hydrogen bonds : angle 4.41489 / 3.18 ( 906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6961 (pp) REVERT: A 68 MET cc_start: 0.5702 (tpt) cc_final: 0.5475 (tpt) REVERT: A 72 PHE cc_start: 0.7880 (m-80) cc_final: 0.7650 (m-80) REVERT: A 73 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8106 (tm) REVERT: A 91 LYS cc_start: 0.8761 (mmtt) cc_final: 0.7664 (mtmt) REVERT: A 135 THR cc_start: 0.9025 (m) cc_final: 0.8813 (p) REVERT: A 195 LEU cc_start: 0.7424 (tp) cc_final: 0.7165 (tt) REVERT: A 206 MET cc_start: 0.8911 (ppp) cc_final: 0.8316 (tmm) REVERT: A 228 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8092 (tt) REVERT: A 276 ASP cc_start: 0.7119 (m-30) cc_final: 0.6786 (m-30) REVERT: A 278 ARG cc_start: 0.7242 (tmt170) cc_final: 0.6883 (mtm-85) REVERT: A 364 TRP cc_start: 0.8616 (OUTLIER) cc_final: 0.7101 (t-100) REVERT: A 466 LYS cc_start: 0.7736 (mttm) cc_final: 0.7303 (mttm) REVERT: A 484 VAL cc_start: 0.7462 (t) cc_final: 0.7175 (p) outliers start: 37 outliers final: 20 residues processed: 132 average time/residue: 0.0395 time to fit residues: 6.8700 Evaluate side-chains 129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.149328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128969 restraints weight = 7630.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132402 restraints weight = 4152.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134819 restraints weight = 2686.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136345 restraints weight = 1963.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137572 restraints weight = 1586.241| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3816 Z= 0.157 Angle : 0.700 12.526 5206 Z= 0.338 Chirality : 0.040 0.137 616 Planarity : 0.005 0.038 643 Dihedral : 4.491 36.668 520 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 8.21 % Allowed : 33.08 % Favored : 58.72 % 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: 1.28 (0.38), residues: 480 helix: 1.60 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.18 (0.55), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.012 0.001 TYR A 214 PHE 0.015 0.001 PHE A 72 TRP 0.015 0.002 TRP A 94 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 3814) covalent geometry : angle 0.69961 / 0.34 ( 5202) SS BOND : bond 0.00068 / 0.03 ( 2) SS BOND : angle 0.90916 / 0.32 ( 4) hydrogen bonds : bond 0.04074 / 2.59 ( 302) hydrogen bonds : angle 4.41105 / 3.16 ( 906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6981 (pp) REVERT: A 72 PHE cc_start: 0.7836 (m-80) cc_final: 0.7578 (m-80) REVERT: A 73 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8317 (tm) REVERT: A 91 LYS cc_start: 0.8784 (mmtt) cc_final: 0.7643 (mtmt) REVERT: A 135 THR cc_start: 0.8992 (m) cc_final: 0.8729 (t) REVERT: A 193 ARG cc_start: 0.6870 (mpt180) cc_final: 0.6577 (mtm-85) REVERT: A 206 MET cc_start: 0.8930 (ppp) cc_final: 0.8324 (tmm) REVERT: A 228 LEU cc_start: 0.8504 (tp) cc_final: 0.8086 (tt) REVERT: A 276 ASP cc_start: 0.7361 (m-30) cc_final: 0.7045 (m-30) REVERT: A 278 ARG cc_start: 0.7192 (tmt170) cc_final: 0.6911 (mtm-85) outliers start: 32 outliers final: 20 residues processed: 133 average time/residue: 0.0498 time to fit residues: 8.5887 Evaluate side-chains 131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129636 restraints weight = 7876.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133169 restraints weight = 4223.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.135560 restraints weight = 2715.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137114 restraints weight = 1979.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138331 restraints weight = 1595.180| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3816 Z= 0.144 Angle : 0.680 12.073 5206 Z= 0.328 Chirality : 0.039 0.139 616 Planarity : 0.005 0.037 643 Dihedral : 4.489 36.430 520 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 8.21 % Allowed : 33.59 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.33 (0.38), residues: 480 helix: 1.62 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -2.12 (0.57), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.014 0.001 TYR A 346 PHE 0.018 0.001 PHE A 183 TRP 0.016 0.002 TRP A 94 HIS 0.005 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 3814) covalent geometry : angle 0.67981 / 0.33 ( 5202) SS BOND : bond 0.00042 / 0.02 ( 2) SS BOND : angle 0.86227 / 0.30 ( 4) hydrogen bonds : bond 0.03871 / 2.50 ( 302) hydrogen bonds : angle 4.40195 / 3.16 ( 906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6982 (pp) REVERT: A 68 MET cc_start: 0.6056 (tpt) cc_final: 0.5304 (tpt) REVERT: A 73 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8246 (tm) REVERT: A 91 LYS cc_start: 0.8749 (mmtt) cc_final: 0.7626 (mtmt) REVERT: A 135 THR cc_start: 0.8986 (m) cc_final: 0.8731 (t) REVERT: A 187 LEU cc_start: 0.8272 (tt) cc_final: 0.7906 (pp) REVERT: A 206 MET cc_start: 0.8908 (ppp) cc_final: 0.8322 (tmm) REVERT: A 228 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 276 ASP cc_start: 0.7322 (m-30) cc_final: 0.7044 (m-30) REVERT: A 278 ARG cc_start: 0.7268 (tmt170) cc_final: 0.6940 (mtm-85) REVERT: A 466 LYS cc_start: 0.7760 (mttm) cc_final: 0.7378 (mttm) outliers start: 32 outliers final: 20 residues processed: 135 average time/residue: 0.0474 time to fit residues: 8.4380 Evaluate side-chains 130 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.152209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131813 restraints weight = 7585.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135505 restraints weight = 4074.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138079 restraints weight = 2594.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139703 restraints weight = 1865.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140772 restraints weight = 1494.412| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3816 Z= 0.152 Angle : 0.722 12.845 5206 Z= 0.342 Chirality : 0.039 0.133 616 Planarity : 0.005 0.037 643 Dihedral : 4.458 33.926 520 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 7.18 % Allowed : 34.62 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.28 (0.38), residues: 480 helix: 1.60 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.15 (0.55), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.016 0.001 TYR A 214 PHE 0.034 0.002 PHE A 72 TRP 0.014 0.002 TRP A 94 HIS 0.005 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 3814) covalent geometry : angle 0.72191 / 0.34 ( 5202) SS BOND : bond 0.00057 / 0.03 ( 2) SS BOND : angle 0.84543 / 0.29 ( 4) hydrogen bonds : bond 0.03912 / 2.53 ( 302) hydrogen bonds : angle 4.45210 / 3.17 ( 906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7093 (pp) REVERT: A 68 MET cc_start: 0.5414 (tpt) cc_final: 0.4919 (tpt) REVERT: A 73 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8199 (tm) REVERT: A 91 LYS cc_start: 0.8748 (mmtt) cc_final: 0.7611 (mtmt) REVERT: A 97 LEU cc_start: 0.8487 (tt) cc_final: 0.8171 (tp) REVERT: A 135 THR cc_start: 0.9007 (m) cc_final: 0.8765 (t) REVERT: A 187 LEU cc_start: 0.8216 (tt) cc_final: 0.7847 (pp) REVERT: A 206 MET cc_start: 0.8950 (ppp) cc_final: 0.8359 (tmm) REVERT: A 214 TYR cc_start: 0.7346 (t80) cc_final: 0.7101 (t80) REVERT: A 228 LEU cc_start: 0.8583 (tp) cc_final: 0.8199 (tt) REVERT: A 276 ASP cc_start: 0.7251 (m-30) cc_final: 0.6960 (m-30) REVERT: A 278 ARG cc_start: 0.7236 (tmt170) cc_final: 0.6940 (mtm-85) REVERT: A 364 TRP cc_start: 0.8653 (OUTLIER) cc_final: 0.7088 (t-100) REVERT: A 466 LYS cc_start: 0.7731 (mttm) cc_final: 0.7346 (mttm) outliers start: 28 outliers final: 21 residues processed: 128 average time/residue: 0.0348 time to fit residues: 5.8572 Evaluate side-chains 132 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132733 restraints weight = 7611.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136462 restraints weight = 4014.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139132 restraints weight = 2503.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140766 restraints weight = 1757.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142138 restraints weight = 1369.006| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3816 Z= 0.152 Angle : 0.727 12.248 5206 Z= 0.346 Chirality : 0.040 0.140 616 Planarity : 0.005 0.038 643 Dihedral : 4.443 32.830 520 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 7.18 % Allowed : 34.10 % Favored : 58.72 % 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: 1.22 (0.38), residues: 480 helix: 1.61 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.42 (0.53), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.010 0.001 TYR A 214 PHE 0.049 0.002 PHE A 72 TRP 0.013 0.001 TRP A 171 HIS 0.005 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 3814) covalent geometry : angle 0.72674 / 0.35 ( 5202) SS BOND : bond 0.00088 / 0.04 ( 2) SS BOND : angle 0.82501 / 0.28 ( 4) hydrogen bonds : bond 0.03848 / 2.50 ( 302) hydrogen bonds : angle 4.48190 / 3.19 ( 906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8131 (tm) REVERT: A 91 LYS cc_start: 0.8775 (mmtt) cc_final: 0.7664 (mtmt) REVERT: A 135 THR cc_start: 0.9021 (m) cc_final: 0.8809 (t) REVERT: A 206 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8767 (ppp) REVERT: A 228 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8167 (tt) REVERT: A 253 MET cc_start: 0.8314 (mtt) cc_final: 0.7957 (mtt) REVERT: A 269 ILE cc_start: 0.8312 (mt) cc_final: 0.7850 (mm) REVERT: A 278 ARG cc_start: 0.7268 (tmt170) cc_final: 0.6935 (mtm-85) REVERT: A 364 TRP cc_start: 0.8716 (OUTLIER) cc_final: 0.7154 (t-100) REVERT: A 466 LYS cc_start: 0.7776 (mttm) cc_final: 0.7399 (mttm) outliers start: 28 outliers final: 20 residues processed: 125 average time/residue: 0.0424 time to fit residues: 7.0524 Evaluate side-chains 127 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.0470 chunk 47 optimal weight: 0.0470 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.154373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134634 restraints weight = 7553.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138450 restraints weight = 3987.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141136 restraints weight = 2479.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142782 restraints weight = 1746.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144207 restraints weight = 1363.861| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3816 Z= 0.142 Angle : 0.747 13.467 5206 Z= 0.353 Chirality : 0.040 0.143 616 Planarity : 0.005 0.038 643 Dihedral : 4.441 33.147 520 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 6.92 % Allowed : 35.90 % Favored : 57.18 % 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: 1.22 (0.38), residues: 480 helix: 1.61 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.42 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.024 0.001 TYR A 214 PHE 0.045 0.002 PHE A 72 TRP 0.015 0.002 TRP A 171 HIS 0.005 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 3814) covalent geometry : angle 0.74661 / 0.35 ( 5202) SS BOND : bond 0.00054 / 0.03 ( 2) SS BOND : angle 0.83015 / 0.27 ( 4) hydrogen bonds : bond 0.03799 / 2.49 ( 302) hydrogen bonds : angle 4.44145 / 3.18 ( 906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7985 (tm) REVERT: A 91 LYS cc_start: 0.8739 (mmtt) cc_final: 0.7642 (mtmt) REVERT: A 135 THR cc_start: 0.9017 (m) cc_final: 0.8805 (t) REVERT: A 187 LEU cc_start: 0.8161 (tt) cc_final: 0.7861 (pp) REVERT: A 228 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8123 (tt) REVERT: A 253 MET cc_start: 0.8287 (mtt) cc_final: 0.7888 (mtt) REVERT: A 269 ILE cc_start: 0.8374 (mt) cc_final: 0.7884 (mm) REVERT: A 278 ARG cc_start: 0.7219 (tmt170) cc_final: 0.6887 (mtm-85) REVERT: A 466 LYS cc_start: 0.7820 (mttm) cc_final: 0.7419 (mttm) outliers start: 27 outliers final: 21 residues processed: 121 average time/residue: 0.0427 time to fit residues: 6.7533 Evaluate side-chains 122 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132642 restraints weight = 7597.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136295 restraints weight = 4044.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138913 restraints weight = 2562.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140757 restraints weight = 1830.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141879 restraints weight = 1424.210| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3816 Z= 0.154 Angle : 0.768 13.606 5206 Z= 0.366 Chirality : 0.042 0.242 616 Planarity : 0.005 0.038 643 Dihedral : 4.503 35.958 520 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 6.41 % Allowed : 35.90 % Favored : 57.69 % 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: 1.16 (0.38), residues: 480 helix: 1.53 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -2.33 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.021 0.001 TYR A 214 PHE 0.023 0.001 PHE A 72 TRP 0.014 0.002 TRP A 171 HIS 0.005 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 ( 3814) covalent geometry : angle 0.76816 / 0.37 ( 5202) SS BOND : bond 0.00077 / 0.04 ( 2) SS BOND : angle 0.83860 / 0.29 ( 4) hydrogen bonds : bond 0.03886 / 2.50 ( 302) hydrogen bonds : angle 4.46604 / 3.18 ( 906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7794 (tm) REVERT: A 91 LYS cc_start: 0.8813 (mmtt) cc_final: 0.7758 (mtmt) REVERT: A 97 LEU cc_start: 0.8535 (tt) cc_final: 0.8243 (tp) REVERT: A 135 THR cc_start: 0.9024 (m) cc_final: 0.8804 (t) REVERT: A 187 LEU cc_start: 0.8254 (tt) cc_final: 0.7941 (pp) REVERT: A 228 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8122 (tt) REVERT: A 269 ILE cc_start: 0.8498 (mt) cc_final: 0.8030 (mm) REVERT: A 278 ARG cc_start: 0.7195 (tmt170) cc_final: 0.6865 (mtm-85) REVERT: A 341 VAL cc_start: 0.7053 (OUTLIER) cc_final: 0.6826 (p) REVERT: A 466 LYS cc_start: 0.7844 (mttm) cc_final: 0.7444 (mttm) REVERT: A 484 VAL cc_start: 0.7355 (t) cc_final: 0.7078 (p) REVERT: A 535 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6610 (m-80) outliers start: 25 outliers final: 21 residues processed: 118 average time/residue: 0.0396 time to fit residues: 6.1997 Evaluate side-chains 129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 535 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.151932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.132174 restraints weight = 7688.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135941 restraints weight = 4084.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138550 restraints weight = 2563.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140224 restraints weight = 1825.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141605 restraints weight = 1439.973| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3816 Z= 0.161 Angle : 0.787 14.000 5206 Z= 0.379 Chirality : 0.042 0.246 616 Planarity : 0.005 0.038 643 Dihedral : 4.543 36.169 520 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.92 % Allowed : 36.15 % Favored : 56.92 % 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: 1.15 (0.38), residues: 480 helix: 1.52 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -2.30 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.036 0.002 TYR A 214 PHE 0.027 0.002 PHE A 72 TRP 0.014 0.002 TRP A 171 HIS 0.005 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 3814) covalent geometry : angle 0.78660 / 0.38 ( 5202) SS BOND : bond 0.00090 / 0.04 ( 2) SS BOND : angle 0.86269 / 0.30 ( 4) hydrogen bonds : bond 0.04000 / 2.59 ( 302) hydrogen bonds : angle 4.51832 / 3.22 ( 906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 638.07 seconds wall clock time: 11 minutes 38.38 seconds (698.38 seconds total)