Starting phenix.real_space_refine on Thu Jul 2 09:33:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7utn_26782/07_2026/7utn_26782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utn_26782/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7utn_26782/07_2026/7utn_26782.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7utn_26782/07_2026/7utn_26782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7utn_26782/07_2026/7utn_26782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utn_26782/07_2026/7utn_26782.map" model { file = "/net/cci-nas-00/data/ceres_data/7utn_26782/07_2026/7utn_26782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utn_26782/07_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-dev-6108/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: {'RNA': 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: 2.17, per 1000 atoms: 0.27 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: 0.74 Conformation dependent library (CDL) restraints added in 280.8 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: 1.16 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: 1.68 Time building geometry restraints manager: 1.00 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=" 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 bond pdb=" C3' DA B 118 " pdb=" O3' DA B 118 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.14e+00 ... (remaining 8630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 12246 1.72 - 3.43: 430 3.43 - 5.15: 55 5.15 - 6.87: 4 6.87 - 8.58: 1 Bond angle restraints: 12736 Sorted by residual: angle pdb=" C4' U C 206 " pdb=" C3' U C 206 " pdb=" O3' U C 206 " ideal model delta sigma weight residual 109.40 117.98 -8.58 1.50e+00 4.44e-01 3.27e+01 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 ... (remaining 12731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 4392 35.57 - 71.15: 253 71.15 - 106.72: 9 106.72 - 142.29: 4 142.29 - 177.87: 10 Dihedral angle restraints: 4668 sinusoidal: 3513 harmonic: 1155 Sorted by residual: dihedral pdb=" O4' C C 60 " pdb=" C1' C C 60 " pdb=" N1 C C 60 " pdb=" C2 C C 60 " ideal model delta sinusoidal sigma weight residual 200.00 36.86 163.14 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' U C 204 " pdb=" C1' U C 204 " pdb=" N1 U C 204 " pdb=" C2 U C 204 " ideal model delta sinusoidal sigma weight residual 200.00 46.30 153.70 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' U C 180 " pdb=" C1' U C 180 " pdb=" N1 U C 180 " pdb=" C2 U C 180 " ideal model delta sinusoidal sigma weight residual -160.00 -28.49 -131.51 1 1.50e+01 4.44e-03 7.09e+01 ... (remaining 4665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1427 0.072 - 0.144: 126 0.144 - 0.216: 10 0.216 - 0.288: 3 0.288 - 0.361: 1 Chirality restraints: 1567 Sorted by residual: chirality pdb=" C3' A C 128 " pdb=" C4' A C 128 " pdb=" O3' A C 128 " pdb=" C2' A C 128 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C2' A C 78 " pdb=" C3' A C 78 " pdb=" O2' A C 78 " pdb=" C1' A C 78 " both_signs ideal model delta sigma weight residual False -2.75 -2.48 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1' G C 121 " pdb=" O4' G C 121 " pdb=" C2' G C 121 " pdb=" N9 G C 121 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.23 2.00e-01 2.50e+01 1.38e+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: 2.130 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.440 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- 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= 0.441 Angle : 0.719 8.584 12736 Z= 0.499 Chirality : 0.044 0.361 1567 Planarity : 0.004 0.056 787 Dihedral : 18.615 177.868 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 0.00697 / 0.44 ( 8635) covalent geometry : angle 0.71873 / 0.50 (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 : 0.193 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: 0.8270 time to fit residues: 26.0199 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 : 0.187 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 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 = 0.3309 r_free = 0.3309 target = 0.084588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.059595 restraints weight = 16867.289| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.42 r_work: 0.2700 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8635 Z= 0.174 Angle : 0.622 6.655 12736 Z= 0.344 Chirality : 0.039 0.287 1567 Planarity : 0.005 0.058 787 Dihedral : 19.013 177.571 3111 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.29 % Allowed : 4.94 % 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: 0.49 (0.40), residues: 393 helix: 1.69 (0.46), residues: 118 sheet: 0.18 (0.72), residues: 55 loop : -0.37 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 363 TYR 0.016 0.001 TYR D 327 PHE 0.008 0.001 PHE D 453 TRP 0.008 0.001 TRP D 161 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 ( 8635) covalent geometry : angle 0.62236 / 0.34 (12736) hydrogen bonds : bond 0.04444 / 2.96 ( 314) hydrogen bonds : angle 3.69521 / 2.66 ( 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 25 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.187 Fit side-chains REVERT: D 102 MET cc_start: 0.9185 (mmt) cc_final: 0.8921 (mmt) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.6783 time to fit residues: 17.3378 Evaluate side-chains 22 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET 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: 5.9990 chunk 25 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.082132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.056936 restraints weight = 16748.044| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.49 r_work: 0.2640 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 8635 Z= 0.336 Angle : 0.676 6.892 12736 Z= 0.373 Chirality : 0.043 0.375 1567 Planarity : 0.005 0.061 787 Dihedral : 19.039 177.765 3111 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.58 % Allowed : 5.81 % 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: 0.46 (0.40), residues: 393 helix: 1.71 (0.46), residues: 118 sheet: -0.17 (0.61), residues: 74 loop : -0.30 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 363 TYR 0.025 0.002 TYR D 327 PHE 0.009 0.001 PHE D 453 TRP 0.009 0.002 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.34 ( 8635) covalent geometry : angle 0.67639 / 0.37 (12736) hydrogen bonds : bond 0.04945 / 3.23 ( 314) hydrogen bonds : angle 3.62893 / 2.62 ( 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 26 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.161 Fit side-chains REVERT: D 73 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8269 (mp0) REVERT: D 102 MET cc_start: 0.9138 (mmt) cc_final: 0.8867 (mmt) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.8759 time to fit residues: 21.9923 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 : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.0040 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.085375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.060332 restraints weight = 17076.731| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.42 r_work: 0.2717 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8635 Z= 0.143 Angle : 0.585 7.187 12736 Z= 0.323 Chirality : 0.037 0.273 1567 Planarity : 0.004 0.056 787 Dihedral : 18.955 177.388 3111 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.16 % Allowed : 6.40 % Favored : 92.44 % 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: 0.71 (0.41), residues: 393 helix: 1.92 (0.46), residues: 119 sheet: 0.07 (0.64), residues: 70 loop : -0.20 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 363 TYR 0.010 0.001 TYR D 484 PHE 0.007 0.001 PHE D 453 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 0.00264 / 0.14 ( 8635) covalent geometry : angle 0.58505 / 0.32 (12736) hydrogen bonds : bond 0.03979 / 2.69 ( 314) hydrogen bonds : angle 3.38054 / 2.43 ( 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 29 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.187 Fit side-chains REVERT: D 33 ARG cc_start: 0.7207 (ttp80) cc_final: 0.6961 (ttp80) REVERT: D 73 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8254 (mp0) REVERT: D 102 MET cc_start: 0.9199 (mmt) cc_final: 0.8945 (mmt) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.7974 time to fit residues: 22.6145 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 : 0.124 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.083356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.058224 restraints weight = 16911.642| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.46 r_work: 0.2667 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8635 Z= 0.256 Angle : 0.619 6.488 12736 Z= 0.342 Chirality : 0.040 0.342 1567 Planarity : 0.005 0.057 787 Dihedral : 18.935 177.548 3111 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.87 % Allowed : 7.27 % Favored : 91.86 % 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: 0.78 (0.41), residues: 393 helix: 2.00 (0.46), residues: 119 sheet: 0.03 (0.64), residues: 70 loop : -0.14 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 363 TYR 0.009 0.001 TYR D 5 PHE 0.008 0.001 PHE D 453 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 0.00505 / 0.26 ( 8635) covalent geometry : angle 0.61916 / 0.34 (12736) hydrogen bonds : bond 0.04453 / 2.95 ( 314) hydrogen bonds : angle 3.41632 / 2.45 ( 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 25 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.194 Fit side-chains REVERT: D 33 ARG cc_start: 0.7187 (ttp80) cc_final: 0.6496 (ptp-110) REVERT: D 73 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8318 (mp0) REVERT: D 102 MET cc_start: 0.9168 (mmt) cc_final: 0.8921 (mmt) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.8721 time to fit residues: 21.0464 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 : 0.191 ------------------------------------------------------------------------------- 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: 3.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.084982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.059930 restraints weight = 16852.905| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.42 r_work: 0.2711 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8635 Z= 0.157 Angle : 0.575 6.648 12736 Z= 0.318 Chirality : 0.037 0.304 1567 Planarity : 0.004 0.054 787 Dihedral : 18.870 177.413 3111 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.16 % Allowed : 6.98 % Favored : 91.86 % 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: 2.14 (0.47), residues: 119 sheet: 0.09 (0.64), residues: 70 loop : -0.07 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 363 TYR 0.009 0.001 TYR D 484 PHE 0.007 0.001 PHE D 453 TRP 0.008 0.001 TRP D 161 HIS 0.002 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 ( 8635) covalent geometry : angle 0.57532 / 0.32 (12736) hydrogen bonds : bond 0.03980 / 2.69 ( 314) hydrogen bonds : angle 3.31201 / 2.37 ( 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 29 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.159 Fit side-chains REVERT: D 33 ARG cc_start: 0.7256 (ttp80) cc_final: 0.6568 (ptp-110) REVERT: D 73 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8293 (mp0) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.8022 time to fit residues: 22.7313 Evaluate side-chains 25 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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: 10.0000 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.083021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.057823 restraints weight = 16858.071| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.43 r_work: 0.2659 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8635 Z= 0.285 Angle : 0.631 6.648 12736 Z= 0.346 Chirality : 0.041 0.351 1567 Planarity : 0.005 0.056 787 Dihedral : 18.902 177.487 3111 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.16 % Allowed : 6.98 % Favored : 91.86 % 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: 2.08 (0.46), residues: 119 sheet: -0.02 (0.64), residues: 70 loop : -0.12 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 363 TYR 0.013 0.001 TYR D 327 PHE 0.008 0.001 PHE D 453 TRP 0.008 0.001 TRP D 161 HIS 0.003 0.001 HIS D 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.28 ( 8635) covalent geometry : angle 0.63103 / 0.35 (12736) hydrogen bonds : bond 0.04611 / 3.06 ( 314) hydrogen bonds : angle 3.41661 / 2.45 ( 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 27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.188 Fit side-chains REVERT: D 33 ARG cc_start: 0.7259 (ttp80) cc_final: 0.6579 (ptp-110) REVERT: D 73 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8290 (mp0) REVERT: D 355 LYS cc_start: 0.8823 (mmpt) cc_final: 0.8516 (mtmp) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.8515 time to fit residues: 22.3505 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 : 0.185 ------------------------------------------------------------------------------- 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: 0.6980 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.085171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.060159 restraints weight = 16874.132| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.42 r_work: 0.2716 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8635 Z= 0.146 Angle : 0.578 6.652 12736 Z= 0.317 Chirality : 0.037 0.286 1567 Planarity : 0.004 0.052 787 Dihedral : 18.840 177.298 3111 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.87 % Allowed : 7.85 % Favored : 91.28 % 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: 1.02 (0.42), residues: 393 helix: 2.27 (0.47), residues: 119 sheet: 0.08 (0.65), residues: 70 loop : -0.00 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 363 TYR 0.010 0.001 TYR D 327 PHE 0.007 0.001 PHE D 40 TRP 0.008 0.001 TRP D 161 HIS 0.003 0.001 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 ( 8635) covalent geometry : angle 0.57845 / 0.32 (12736) hydrogen bonds : bond 0.03986 / 2.69 ( 314) hydrogen bonds : angle 3.33187 / 2.39 ( 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 29 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.197 Fit side-chains REVERT: D 33 ARG cc_start: 0.7243 (ttp80) cc_final: 0.6992 (ttp80) REVERT: D 37 ARG cc_start: 0.8390 (ttp80) cc_final: 0.7845 (ttp-110) REVERT: D 73 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8278 (mp0) REVERT: D 392 LYS cc_start: 0.8621 (mptt) cc_final: 0.8388 (mmtp) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.8503 time to fit residues: 24.0823 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 : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.083350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.058128 restraints weight = 16813.067| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 1.49 r_work: 0.2663 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8635 Z= 0.273 Angle : 0.619 6.593 12736 Z= 0.340 Chirality : 0.040 0.344 1567 Planarity : 0.004 0.054 787 Dihedral : 18.842 177.446 3111 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.58 % Allowed : 8.14 % Favored : 91.28 % 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: 0.94 (0.42), residues: 393 helix: 2.20 (0.46), residues: 119 sheet: 0.00 (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 0.015 0.001 TYR D 327 PHE 0.007 0.001 PHE D 453 TRP 0.007 0.001 TRP D 161 HIS 0.003 0.001 HIS D 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.27 ( 8635) covalent geometry : angle 0.61886 / 0.34 (12736) hydrogen bonds : bond 0.04563 / 3.03 ( 314) hydrogen bonds : angle 3.39628 / 2.44 ( 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 26 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.197 Fit side-chains REVERT: D 33 ARG cc_start: 0.7186 (ttp80) cc_final: 0.6939 (ttp80) REVERT: D 37 ARG cc_start: 0.8422 (ttp80) cc_final: 0.7764 (ttp-110) REVERT: D 73 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8242 (mp0) REVERT: D 355 LYS cc_start: 0.8909 (mmpt) cc_final: 0.8629 (mtmp) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.8549 time to fit residues: 21.5478 Evaluate side-chains 26 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.084472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.059348 restraints weight = 16814.733| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.42 r_work: 0.2694 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8635 Z= 0.167 Angle : 0.589 6.832 12736 Z= 0.323 Chirality : 0.037 0.317 1567 Planarity : 0.004 0.056 787 Dihedral : 18.852 177.454 3111 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.58 % Allowed : 8.43 % 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: 1.01 (0.42), residues: 393 helix: 2.26 (0.46), residues: 119 sheet: 0.04 (0.65), residues: 70 loop : 0.01 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 363 TYR 0.010 0.001 TYR D 484 PHE 0.007 0.001 PHE D 453 TRP 0.009 0.001 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 ( 8635) covalent geometry : angle 0.58856 / 0.32 (12736) hydrogen bonds : bond 0.04234 / 2.81 ( 314) hydrogen bonds : angle 3.34187 / 2.39 ( 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 28 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.195 Fit side-chains REVERT: D 33 ARG cc_start: 0.7259 (ttp80) cc_final: 0.7009 (ttp80) REVERT: D 37 ARG cc_start: 0.8457 (ttp80) cc_final: 0.7878 (ttp-110) REVERT: D 73 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8280 (mp0) REVERT: D 355 LYS cc_start: 0.8919 (mmpt) cc_final: 0.8636 (mtmp) REVERT: D 392 LYS cc_start: 0.8627 (mptt) cc_final: 0.8395 (mmtp) outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.8336 time to fit residues: 22.7246 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 : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 49 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 87 ASN ** 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 = 0.3263 r_free = 0.3263 target = 0.082361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.057180 restraints weight = 16839.447| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 1.50 r_work: 0.2627 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 8635 Z= 0.346 Angle : 0.660 6.912 12736 Z= 0.360 Chirality : 0.043 0.361 1567 Planarity : 0.005 0.056 787 Dihedral : 18.915 177.469 3111 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 (0.42), residues: 393 helix: 2.05 (0.46), residues: 119 sheet: -0.06 (0.65), residues: 70 loop : -0.10 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 363 TYR 0.015 0.002 TYR D 327 PHE 0.008 0.001 PHE D 453 TRP 0.008 0.001 TRP D 161 HIS 0.003 0.001 HIS D 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.35 ( 8635) covalent geometry : angle 0.66010 / 0.36 (12736) hydrogen bonds : bond 0.04920 / 3.25 ( 314) hydrogen bonds : angle 3.46375 / 2.48 ( 694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2682.51 seconds wall clock time: 46 minutes 37.41 seconds (2797.41 seconds total)