Starting phenix.real_space_refine on Fri Sep 11 06:08:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7utn_26782/09_2026/7utn_26782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utn_26782/09_2026/7utn_26782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7utn_26782/09_2026/7utn_26782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utn_26782/09_2026/7utn_26782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7utn_26782/09_2026/7utn_26782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utn_26782/09_2026/7utn_26782.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7utn_26782/09_2026/7utn_26782.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7utn_26782/09_2026/7utn_26782.cif" } resolution = 2.74 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= 0.026 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 P 228 5.49 5 S 21 5.16 5 C 4183 2.51 5 N 1470 2.21 5 O 2101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8003 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3174 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 378} Chain breaks: 1 Chain: "C" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3937 Classifications: {'RNAv2': 184} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 90, 'rna3p_pyr': 68} Link IDs: {'rna2p': 25, 'rna3p': 158} Chain breaks: 2 Chain: "A" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 579 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "B" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 313 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Time building chain proxies: 1.93, per 1000 atoms: 0.24 Number of scatterers: 8003 At special positions: 0 Unit cell: (90.95, 105.93, 131.61, 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) S 21 16.00 P 228 15.00 O 2101 8.00 N 1470 7.00 C 4183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.80 Conformation dependent library (CDL) restraints added in 127.3 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 6 sheets defined 30.0% alpha, 20.4% beta 76 base pairs and 137 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'D' and resid 21 through 29 Processing helix chain 'D' and resid 88 through 109 removed outlier: 4.313A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 163 through 184 removed outlier: 3.662A pdb=" N ILE D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 314 Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'D' and resid 340 through 348 removed outlier: 4.588A pdb=" N TYR D 344 " --> pdb=" O TYR D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7 removed outlier: 6.264A pdb=" N TYR D 5 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU D 44 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 7 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR D 41 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.231A pdb=" N VAL D 189 " --> pdb=" O CYS D 319 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR D 321 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU D 191 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU D 57 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLU D 192 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE D 59 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 79 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 369 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N MET D 366 " --> pdb=" O TYR D 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 131 Processing sheet with id=AA4, first strand: chain 'D' and resid 378 through 380 removed outlier: 6.559A pdb=" N GLN D 432 " --> pdb=" O HIS D 379 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 392 through 395 removed outlier: 6.610A pdb=" N TYR D 387 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 476 through 478 removed outlier: 4.836A pdb=" N VAL D 466 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLY D 460 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR D 468 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER D 458 " --> pdb=" O TYR D 468 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 470 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE D 444 " --> pdb=" O LEU D 485 " (cutoff:3.500A) 118 hydrogen bonds defined for protein. 330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 196 hydrogen bonds 364 hydrogen bond angles 0 basepair planarities 76 basepair parallelities 137 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1144 1.33 - 1.45: 3372 1.45 - 1.56: 3635 1.56 - 1.68: 451 1.68 - 1.80: 33 Bond restraints: 8635 Sorted by residual: bond pdb=" C3' DT B 117 " pdb=" O3' DT B 117 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" O3' U C 205 " pdb=" P U C 206 " ideal model delta sigma weight residual 1.607 1.572 0.035 1.20e-02 6.94e+03 8.59e+00 bond pdb=" C3' DG B 119 " pdb=" O3' DG B 119 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.43e+00 bond pdb=" C3' DA B 115 " pdb=" O3' DA B 115 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 8.06e+00 bond pdb=" C3' DC B 116 " pdb=" O3' DC B 116 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.24e+00 ... (remaining 8630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 11770 1.75 - 3.51: 815 3.51 - 5.26: 138 5.26 - 7.01: 11 7.01 - 8.77: 2 Bond angle restraints: 12736 Sorted by residual: angle pdb=" O4' DT A 24 " pdb=" C4' DT A 24 " pdb=" C3' DT A 24 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT A 32 " pdb=" C4 DT A 32 " pdb=" O4 DT A 32 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" O5' DT A 12 " pdb=" C5' DT A 12 " pdb=" C4' DT A 12 " ideal model delta sigma weight residual 109.40 112.87 -3.47 8.00e-01 1.56e+00 1.88e+01 angle pdb=" N3 DT A 30 " pdb=" C4 DT A 30 " pdb=" O4 DT A 30 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" O4' DC A 25 " pdb=" C4' DC A 25 " pdb=" C3' DC A 25 " ideal model delta sigma weight residual 106.00 103.44 2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 12731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 4168 35.16 - 70.33: 471 70.33 - 105.49: 24 105.49 - 140.65: 0 140.65 - 175.82: 5 Dihedral angle restraints: 4668 sinusoidal: 3513 harmonic: 1155 Sorted by residual: dihedral pdb=" C4' U C 206 " pdb=" C3' U C 206 " pdb=" C2' U C 206 " pdb=" C1' U C 206 " ideal model delta sinusoidal sigma weight residual 36.34 -42.63 78.97 1 3.10e+00 1.04e-01 8.08e+02 dihedral pdb=" C4' A C 165 " pdb=" C3' A C 165 " pdb=" C2' A C 165 " pdb=" C1' A C 165 " ideal model delta sinusoidal sigma weight residual 36.34 -39.99 76.33 1 3.10e+00 1.04e-01 7.63e+02 dihedral pdb=" C4' A C 207 " pdb=" C3' A C 207 " pdb=" C2' A C 207 " pdb=" C1' A C 207 " ideal model delta sinusoidal sigma weight residual 36.34 -38.07 74.41 1 3.10e+00 1.04e-01 7.31e+02 ... (remaining 4665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1204 0.073 - 0.146: 117 0.146 - 0.220: 134 0.220 - 0.293: 105 0.293 - 0.366: 7 Chirality restraints: 1567 Sorted by residual: chirality pdb=" P A C 207 " pdb=" OP1 A C 207 " pdb=" OP2 A C 207 " pdb=" O5' A C 207 " both_signs ideal model delta sigma weight residual True 2.17 -2.54 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C2' A C 128 " pdb=" C3' A C 128 " pdb=" O2' A C 128 " pdb=" C1' A C 128 " both_signs ideal model delta sigma weight residual False -2.79 -2.46 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C3' A C 165 " pdb=" C4' A C 165 " pdb=" O3' A C 165 " pdb=" C2' A C 165 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1564 not shown) Planarity restraints: 787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 78 " -0.042 2.00e-02 2.50e+03 2.12e-02 1.24e+01 pdb=" N9 A C 78 " 0.055 2.00e-02 2.50e+03 pdb=" C8 A C 78 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A C 78 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A C 78 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A C 78 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A C 78 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A C 78 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A C 78 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 78 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A C 78 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 91 " -0.034 2.00e-02 2.50e+03 1.45e-02 6.27e+00 pdb=" N9 G C 91 " 0.034 2.00e-02 2.50e+03 pdb=" C8 G C 91 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G C 91 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 91 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G C 91 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G C 91 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 91 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G C 91 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 163 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO D 164 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " -0.031 5.00e-02 4.00e+02 ... (remaining 784 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 226 2.64 - 3.21: 6504 3.21 - 3.77: 15156 3.77 - 4.34: 20706 4.34 - 4.90: 28300 Nonbonded interactions: 70892 Sorted by model distance: nonbonded pdb=" O2' A C 78 " pdb=" O4' G C 79 " model vdw 2.080 3.040 nonbonded pdb=" O4 U C 30 " pdb=" N6 A C 46 " model vdw 2.215 3.120 nonbonded pdb=" NH1 ARG D 115 " pdb=" OP2 C C 58 " model vdw 2.223 3.120 nonbonded pdb=" OH TYR D 46 " pdb=" OP1 U C 206 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN D 487 " pdb=" N ASN D 488 " model vdw 2.321 3.120 ... (remaining 70887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 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 : 0.007 0.043 8635 Z= 0.443 Angle : 0.958 8.767 12736 Z= 0.527 Chirality : 0.097 0.366 1567 Planarity : 0.004 0.056 787 Dihedral : 21.619 175.817 3924 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.01 (0.40), residues: 393 helix: 1.09 (0.47), residues: 117 sheet: -0.44 (0.62), residues: 63 loop : -0.40 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 486 TYR 0.010 0.001 TYR D 5 PHE 0.010 0.002 PHE D 453 TRP 0.012 0.002 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.44 ( 8635) covalent geometry : angle 0.95807 / 0.53 (12736) hydrogen bonds : bond 0.09493 / 5.18 ( 314) hydrogen bonds : angle 5.43414 / 3.90 ( 694) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.191 Fit side-chains REVERT: D 102 MET cc_start: 0.8633 (mmt) cc_final: 0.8320 (mmt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.8527 time to fit residues: 26.8058 Evaluate side-chains 22 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 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 = 0.3337 r_free = 0.3337 target = 0.086276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.061304 restraints weight = 16924.233| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.42 r_work: 0.2735 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8635 Z= 0.263 Angle : 1.443 21.480 12736 Z= 0.593 Chirality : 0.135 1.332 1567 Planarity : 0.005 0.058 787 Dihedral : 20.788 179.122 3111 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.58 % Allowed : 4.65 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.47 (0.40), residues: 393 helix: 1.66 (0.46), residues: 118 sheet: 0.16 (0.72), residues: 55 loop : -0.35 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 363 TYR 0.014 0.001 TYR D 327 PHE 0.008 0.001 PHE D 453 TRP 0.008 0.001 TRP D 161 HIS 0.006 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.26 ( 8635) covalent geometry : angle 1.44277 / 0.59 (12736) hydrogen bonds : bond 0.04610 / 3.07 ( 314) hydrogen bonds : angle 3.73325 / 2.69 ( 694) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.194 Fit side-chains REVERT: D 102 MET cc_start: 0.9192 (mmt) cc_final: 0.8926 (mmt) outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.8007 time to fit residues: 21.9106 Evaluate side-chains 23 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 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 = 0.3304 r_free = 0.3304 target = 0.084555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.059383 restraints weight = 16820.291| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.44 r_work: 0.2686 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 8635 Z= 0.350 Angle : 1.194 15.721 12736 Z= 0.506 Chirality : 0.110 1.236 1567 Planarity : 0.005 0.059 787 Dihedral : 20.635 175.558 3111 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.87 % Allowed : 5.52 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.60 (0.40), residues: 393 helix: 1.75 (0.46), residues: 118 sheet: -0.08 (0.66), residues: 63 loop : -0.16 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 486 TYR 0.027 0.002 TYR D 327 PHE 0.009 0.001 PHE D 453 TRP 0.010 0.002 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.35 ( 8635) covalent geometry : angle 1.19413 / 0.51 (12736) hydrogen bonds : bond 0.05024 / 3.33 ( 314) hydrogen bonds : angle 3.62459 / 2.61 ( 694) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.190 Fit side-chains REVERT: D 102 MET cc_start: 0.9166 (mmt) cc_final: 0.8881 (mmt) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.8677 time to fit residues: 20.9521 Evaluate side-chains 23 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.062895 restraints weight = 17110.038| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.43 r_work: 0.2770 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8635 Z= 0.188 Angle : 1.030 13.925 12736 Z= 0.436 Chirality : 0.090 1.002 1567 Planarity : 0.004 0.056 787 Dihedral : 20.654 176.864 3111 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.87 % Allowed : 6.98 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.84 (0.41), residues: 393 helix: 1.94 (0.45), residues: 121 sheet: -0.01 (0.67), residues: 63 loop : -0.01 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 363 TYR 0.008 0.001 TYR D 484 PHE 0.011 0.001 PHE D 40 TRP 0.008 0.001 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 ( 8635) covalent geometry : angle 1.02973 / 0.44 (12736) hydrogen bonds : bond 0.04295 / 2.94 ( 314) hydrogen bonds : angle 3.42976 / 2.47 ( 694) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.176 Fit side-chains REVERT: D 33 ARG cc_start: 0.7284 (ttp80) cc_final: 0.7038 (ttp80) REVERT: D 37 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8195 (ttp-110) REVERT: D 102 MET cc_start: 0.9204 (mmt) cc_final: 0.8942 (mmt) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.7915 time to fit residues: 21.6325 Evaluate side-chains 24 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 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 = 0.3323 r_free = 0.3323 target = 0.085537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.060278 restraints weight = 16945.504| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.44 r_work: 0.2704 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8635 Z= 0.307 Angle : 1.067 15.024 12736 Z= 0.455 Chirality : 0.093 1.051 1567 Planarity : 0.005 0.058 787 Dihedral : 20.588 174.873 3111 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.87 % Allowed : 8.14 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.80 (0.41), residues: 393 helix: 1.87 (0.46), residues: 119 sheet: -0.04 (0.67), residues: 63 loop : 0.01 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 363 TYR 0.010 0.001 TYR D 327 PHE 0.008 0.001 PHE D 453 TRP 0.008 0.002 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.31 ( 8635) covalent geometry : angle 1.06745 / 0.46 (12736) hydrogen bonds : bond 0.04822 / 3.21 ( 314) hydrogen bonds : angle 3.46959 / 2.50 ( 694) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.188 Fit side-chains REVERT: D 33 ARG cc_start: 0.7292 (ttp80) cc_final: 0.7071 (ttp80) REVERT: D 102 MET cc_start: 0.9193 (mmt) cc_final: 0.8930 (mmt) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.8243 time to fit residues: 21.6283 Evaluate side-chains 26 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.0010 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 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 = 0.3386 r_free = 0.3386 target = 0.088934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.063986 restraints weight = 16922.491| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.42 r_work: 0.2799 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8635 Z= 0.165 Angle : 0.961 12.617 12736 Z= 0.407 Chirality : 0.081 0.846 1567 Planarity : 0.004 0.055 787 Dihedral : 20.638 175.405 3111 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.16 % Allowed : 7.85 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.91 (0.41), residues: 393 helix: 2.03 (0.46), residues: 121 sheet: 0.26 (0.75), residues: 54 loop : -0.07 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 363 TYR 0.009 0.001 TYR D 484 PHE 0.010 0.001 PHE D 40 TRP 0.007 0.001 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 ( 8635) covalent geometry : angle 0.96081 / 0.41 (12736) hydrogen bonds : bond 0.04191 / 2.88 ( 314) hydrogen bonds : angle 3.34856 / 2.41 ( 694) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.189 Fit side-chains REVERT: D 37 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7927 (ttp-110) REVERT: D 73 GLU cc_start: 0.8154 (mp0) cc_final: 0.7854 (mp0) REVERT: D 102 MET cc_start: 0.9213 (mmt) cc_final: 0.8975 (mmt) REVERT: D 392 LYS cc_start: 0.8649 (mptt) cc_final: 0.8421 (mmtp) outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.7039 time to fit residues: 21.5970 Evaluate side-chains 27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 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 = 0.3408 r_free = 0.3408 target = 0.088476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.063551 restraints weight = 17390.432| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.49 r_work: 0.2809 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8635 Z= 0.277 Angle : 0.994 13.415 12736 Z= 0.424 Chirality : 0.085 0.868 1567 Planarity : 0.005 0.056 787 Dihedral : 20.559 173.515 3111 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.87 % Allowed : 8.43 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.97 (0.42), residues: 393 helix: 1.99 (0.46), residues: 121 sheet: 0.04 (0.69), residues: 63 loop : 0.11 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 363 TYR 0.010 0.001 TYR D 327 PHE 0.007 0.001 PHE D 453 TRP 0.006 0.001 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.28 ( 8635) covalent geometry : angle 0.99355 / 0.42 (12736) hydrogen bonds : bond 0.04630 / 3.12 ( 314) hydrogen bonds : angle 3.39526 / 2.44 ( 694) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.181 Fit side-chains REVERT: D 37 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8059 (ttp-110) REVERT: D 73 GLU cc_start: 0.8219 (mp0) cc_final: 0.7895 (mp0) REVERT: D 392 LYS cc_start: 0.8757 (mptt) cc_final: 0.8529 (mmtp) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.8369 time to fit residues: 25.4764 Evaluate side-chains 29 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 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 = 0.3431 r_free = 0.3431 target = 0.089860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.064943 restraints weight = 17321.697| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.50 r_work: 0.2841 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8635 Z= 0.184 Angle : 0.951 12.361 12736 Z= 0.407 Chirality : 0.081 0.790 1567 Planarity : 0.004 0.055 787 Dihedral : 20.606 173.859 3111 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.03 % Allowed : 7.56 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.03 (0.42), residues: 393 helix: 2.04 (0.46), residues: 121 sheet: 0.06 (0.69), residues: 63 loop : 0.16 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 363 TYR 0.009 0.001 TYR D 484 PHE 0.007 0.001 PHE D 40 TRP 0.007 0.001 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 ( 8635) covalent geometry : angle 0.95087 / 0.41 (12736) hydrogen bonds : bond 0.04350 / 2.94 ( 314) hydrogen bonds : angle 3.36320 / 2.42 ( 694) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.200 Fit side-chains REVERT: D 37 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8077 (ttp-110) REVERT: D 355 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8482 (mtmp) REVERT: D 392 LYS cc_start: 0.8730 (mptt) cc_final: 0.8497 (mmtp) outliers start: 7 outliers final: 4 residues processed: 30 average time/residue: 0.8041 time to fit residues: 25.3564 Evaluate side-chains 31 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 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 = 0.3404 r_free = 0.3404 target = 0.088282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.063206 restraints weight = 17334.379| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.49 r_work: 0.2797 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8635 Z= 0.283 Angle : 1.000 12.033 12736 Z= 0.429 Chirality : 0.084 0.767 1567 Planarity : 0.005 0.056 787 Dihedral : 20.590 172.933 3111 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.45 % Allowed : 8.43 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.82 (0.41), residues: 393 helix: 1.96 (0.47), residues: 119 sheet: 0.02 (0.65), residues: 70 loop : -0.04 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 363 TYR 0.016 0.001 TYR D 327 PHE 0.007 0.001 PHE D 453 TRP 0.006 0.001 TRP D 161 HIS 0.003 0.001 HIS D 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.28 ( 8635) covalent geometry : angle 0.99981 / 0.43 (12736) hydrogen bonds : bond 0.04766 / 3.20 ( 314) hydrogen bonds : angle 3.41913 / 2.45 ( 694) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.189 Fit side-chains REVERT: D 73 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8348 (mp0) REVERT: D 355 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8494 (mtmp) REVERT: D 392 LYS cc_start: 0.8774 (mptt) cc_final: 0.8547 (mmtp) outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.8022 time to fit residues: 25.2623 Evaluate side-chains 29 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 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 = 0.3428 r_free = 0.3428 target = 0.089593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.064713 restraints weight = 17217.556| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.46 r_work: 0.2831 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8635 Z= 0.199 Angle : 0.957 11.686 12736 Z= 0.411 Chirality : 0.081 0.733 1567 Planarity : 0.005 0.056 787 Dihedral : 20.617 172.970 3111 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.16 % Allowed : 9.30 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.91 (0.41), residues: 393 helix: 1.99 (0.46), residues: 121 sheet: 0.07 (0.65), residues: 70 loop : 0.03 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 363 TYR 0.011 0.001 TYR D 327 PHE 0.007 0.001 PHE D 453 TRP 0.008 0.001 TRP D 161 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 ( 8635) covalent geometry : angle 0.95660 / 0.41 (12736) hydrogen bonds : bond 0.04506 / 3.01 ( 314) hydrogen bonds : angle 3.38503 / 2.43 ( 694) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: D 37 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8015 (ttp-110) REVERT: D 355 LYS cc_start: 0.8795 (mmpt) cc_final: 0.8488 (mtmp) REVERT: D 392 LYS cc_start: 0.8781 (mptt) cc_final: 0.8555 (mmtp) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.7753 time to fit residues: 24.4419 Evaluate side-chains 29 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 68 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.061579 restraints weight = 17226.912| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.45 r_work: 0.2765 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 8635 Z= 0.383 Angle : 1.072 12.944 12736 Z= 0.460 Chirality : 0.090 0.826 1567 Planarity : 0.005 0.061 787 Dihedral : 20.631 172.632 3111 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.87 % Allowed : 9.59 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.67 (0.41), residues: 393 helix: 1.77 (0.46), residues: 119 sheet: -0.04 (0.65), residues: 70 loop : -0.10 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 363 TYR 0.018 0.002 TYR D 327 PHE 0.008 0.001 PHE D 453 TRP 0.007 0.001 TRP D 161 HIS 0.004 0.001 HIS D 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.38 ( 8635) covalent geometry : angle 1.07237 / 0.46 (12736) hydrogen bonds : bond 0.05322 / 3.55 ( 314) hydrogen bonds : angle 3.50986 / 2.52 ( 694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2875.77 seconds wall clock time: 49 minutes 47.71 seconds (2987.71 seconds total)