Starting phenix.real_space_refine on Fri Jul 3 17:53:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uin_26550/07_2026/7uin_26550.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uin_26550/07_2026/7uin_26550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uin_26550/07_2026/7uin_26550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uin_26550/07_2026/7uin_26550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uin_26550/07_2026/7uin_26550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uin_26550/07_2026/7uin_26550.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uin_26550/07_2026/7uin_26550.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uin_26550/07_2026/7uin_26550.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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: 6 Type Number sf(0) Gaussians P 578 5.49 5 Mg 28 5.21 5 S 21 5.16 5 C 7546 2.51 5 N 2869 2.21 5 O 4543 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: 15585 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 11639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 11639 Classifications: {'RNA': 541} Modifications used: {'rna2p_pur': 38, 'rna2p_pyr': 10, 'rna3p_pur': 290, 'rna3p_pyr': 203} Link IDs: {'rna2p': 47, 'rna3p': 493} Chain breaks: 5 Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3133 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 2 Chain: "A" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 759 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Unusual residues: {' MG': 28, 'NH4': 2} Classifications: {'undetermined': 30, 'water': 23} Link IDs: {None: 52} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.40, per 1000 atoms: 0.22 Number of scatterers: 15585 At special positions: 0 Unit cell: (99.008, 158.08, 158.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 578 15.00 Mg 28 11.99 O 4543 8.00 N 2869 7.00 C 7546 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: 1.11 Conformation dependent library (CDL) restraints added in 338.7 milliseconds 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 71.3% alpha, 5.9% beta 205 base pairs and 342 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'D' and resid 5 through 11 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 38 through 57 removed outlier: 4.618A pdb=" N GLU D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 103 Proline residue: D 100 - end of helix Processing helix chain 'D' and resid 118 through 133 removed outlier: 3.754A pdb=" N ALA D 122 " --> pdb=" O CYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 150 through 162 removed outlier: 3.733A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.511A pdb=" N SER D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.917A pdb=" N LEU D 201 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 252 Processing helix chain 'D' and resid 266 through 270 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 313 through 333 Processing helix chain 'D' and resid 337 through 361 Processing helix chain 'D' and resid 362 through 373 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 389 through 396 removed outlier: 3.715A pdb=" N LYS D 396 " --> pdb=" O TYR D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 404 through 412 Processing helix chain 'D' and resid 415 through 424 Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 223 removed outlier: 3.948A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 275 through 279 201 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 501 hydrogen bonds 792 hydrogen bond angles 0 basepair planarities 205 basepair parallelities 342 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.13: 1 1.13 - 1.43: 9395 1.43 - 1.73: 7647 1.73 - 2.04: 34 2.04 - 2.34: 1 Bond restraints: 17078 Sorted by residual: bond pdb=" CG PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 1.503 0.828 0.675 3.40e-02 8.65e+02 3.95e+02 bond pdb=" CB PRO D 281 " pdb=" CG PRO D 281 " ideal model delta sigma weight residual 1.492 2.337 -0.845 5.00e-02 4.00e+02 2.86e+02 bond pdb=" N PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 1.473 1.595 -0.122 1.40e-02 5.10e+03 7.65e+01 bond pdb=" C1' DC A 6 " pdb=" N1 DC A 6 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.42e+01 bond pdb=" N PRO D 281 " pdb=" CA PRO D 281 " ideal model delta sigma weight residual 1.471 1.397 0.074 1.32e-02 5.74e+03 3.15e+01 ... (remaining 17073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.20: 25915 21.20 - 42.41: 2 42.41 - 63.61: 0 63.61 - 84.81: 0 84.81 - 106.02: 1 Bond angle restraints: 25918 Sorted by residual: angle pdb=" CB PRO D 281 " pdb=" CG PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 106.10 0.08 106.02 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO D 281 " pdb=" N PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 112.00 89.42 22.58 1.40e+00 5.10e-01 2.60e+02 angle pdb=" N PRO D 281 " pdb=" CA PRO D 281 " pdb=" CB PRO D 281 " ideal model delta sigma weight residual 103.48 89.59 13.89 1.00e+00 1.00e+00 1.93e+02 angle pdb=" CA PRO D 62 " pdb=" N PRO D 62 " pdb=" CD PRO D 62 " ideal model delta sigma weight residual 112.00 94.92 17.08 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CA PRO D 281 " pdb=" CB PRO D 281 " pdb=" CG PRO D 281 " ideal model delta sigma weight residual 104.50 90.46 14.04 1.90e+00 2.77e-01 5.46e+01 ... (remaining 25913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 8126 35.84 - 71.68: 622 71.68 - 107.51: 60 107.51 - 143.35: 8 143.35 - 179.19: 10 Dihedral angle restraints: 8826 sinusoidal: 7702 harmonic: 1124 Sorted by residual: dihedral pdb=" O4' U B 2 " pdb=" C1' U B 2 " pdb=" N1 U B 2 " pdb=" C2 U B 2 " ideal model delta sinusoidal sigma weight residual 200.00 46.39 153.61 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' C B 439 " pdb=" C1' C B 439 " pdb=" N1 C B 439 " pdb=" C2 C B 439 " ideal model delta sinusoidal sigma weight residual 200.00 48.62 151.38 1 1.50e+01 4.44e-03 8.01e+01 dihedral pdb=" O4' C B 440 " pdb=" C1' C B 440 " pdb=" N1 C B 440 " pdb=" C2 C B 440 " ideal model delta sinusoidal sigma weight residual 232.00 79.74 152.26 1 1.70e+01 3.46e-03 6.26e+01 ... (remaining 8823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3097 0.087 - 0.175: 194 0.175 - 0.262: 15 0.262 - 0.350: 9 0.350 - 0.437: 3 Chirality restraints: 3318 Sorted by residual: chirality pdb=" CA PRO D 281 " pdb=" N PRO D 281 " pdb=" C PRO D 281 " pdb=" CB PRO D 281 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CB ILE D 168 " pdb=" CA ILE D 168 " pdb=" CG1 ILE D 168 " pdb=" CG2 ILE D 168 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C1' A B 370 " pdb=" O4' A B 370 " pdb=" C2' A B 370 " pdb=" N9 A B 370 " both_signs ideal model delta sigma weight residual False 2.46 2.08 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 3315 not shown) Planarity restraints: 1121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 47 " 0.032 2.00e-02 2.50e+03 6.26e-02 3.92e+01 pdb=" CG ASN D 47 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN D 47 " 0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN D 47 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 258 " 0.024 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" CG ASN D 258 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN D 258 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN D 258 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 61 " -0.078 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO D 62 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO D 62 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 62 " -0.058 5.00e-02 4.00e+02 ... (remaining 1118 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 11 2.16 - 2.85: 4618 2.85 - 3.53: 21472 3.53 - 4.22: 52655 4.22 - 4.90: 65823 Nonbonded interactions: 144579 Sorted by model distance: nonbonded pdb=" O3' U B 638 " pdb="MG MG B 701 " model vdw 1.477 2.170 nonbonded pdb=" OP1 C B 581 " pdb="MG MG B 701 " model vdw 1.870 2.170 nonbonded pdb=" OP2 A B 559 " pdb="MG MG B 703 " model vdw 2.041 2.170 nonbonded pdb=" OP1 G B 247 " pdb="MG MG B 705 " model vdw 2.056 2.170 nonbonded pdb=" OP2 A B 157 " pdb="MG MG B 708 " model vdw 2.080 2.170 ... (remaining 144574 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: 5.580 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: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.250 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.010 0.845 17078 Z= 0.406 Angle : 1.215 106.017 25918 Z= 0.594 Chirality : 0.049 0.437 3318 Planarity : 0.009 0.108 1121 Dihedral : 19.785 179.187 8102 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 2.93 % Allowed : 36.36 % Favored : 60.70 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.53 % 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: -1.14 (0.37), residues: 381 helix: -0.53 (0.28), residues: 253 sheet: 0.31 (0.92), residues: 24 loop : -1.20 (0.56), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 217 TYR 0.029 0.003 TYR D 385 PHE 0.021 0.005 PHE D 298 TRP 0.011 0.002 TRP D 357 HIS 0.016 0.004 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.01022 / 0.41 (17078) covalent geometry : angle 1.21452 / 0.59 (25918) hydrogen bonds : bond 0.12652 / 7.50 ( 702) hydrogen bonds : angle 5.82068 / 3.46 ( 1383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.292 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.6419 time to fit residues: 41.9256 Evaluate side-chains 40 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 10.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 120 GLN D 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.200605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.154286 restraints weight = 20332.849| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 0.86 r_work: 0.3585 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 17078 Z= 0.222 Angle : 0.721 9.177 25918 Z= 0.375 Chirality : 0.039 0.260 3318 Planarity : 0.007 0.139 1121 Dihedral : 19.227 179.586 7310 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.89 % Favored : 96.59 % Rotamer: Outliers : 7.62 % Allowed : 31.96 % Favored : 60.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -0.11 (0.40), residues: 381 helix: 0.24 (0.30), residues: 258 sheet: 0.29 (0.98), residues: 24 loop : -0.67 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 389 TYR 0.026 0.002 TYR D 385 PHE 0.018 0.003 PHE D 298 TRP 0.010 0.002 TRP D 357 HIS 0.005 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.22 (17078) covalent geometry : angle 0.72059 / 0.38 (25918) hydrogen bonds : bond 0.07241 / 4.28 ( 702) hydrogen bonds : angle 3.59862 / 2.07 ( 1383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 42 time to evaluate : 0.316 Fit side-chains REVERT: D 63 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: D 300 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7947 (mmmt) REVERT: D 326 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8478 (mtt-85) REVERT: D 358 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8573 (tptt) outliers start: 26 outliers final: 6 residues processed: 63 average time/residue: 0.6501 time to fit residues: 45.0860 Evaluate side-chains 46 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 362 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 120 GLN ** D 151 HIS ** 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 = 0.4302 r_free = 0.4302 target = 0.194586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.150511 restraints weight = 20240.795| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.11 r_work: 0.3455 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 17078 Z= 0.361 Angle : 0.821 10.809 25918 Z= 0.423 Chirality : 0.045 0.312 3318 Planarity : 0.007 0.143 1121 Dihedral : 19.255 179.051 7302 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.41 % Favored : 96.33 % Rotamer: Outliers : 10.56 % Allowed : 29.03 % Favored : 60.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.41), residues: 381 helix: 0.20 (0.31), residues: 253 sheet: 0.86 (1.02), residues: 24 loop : -1.37 (0.59), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 389 TYR 0.039 0.004 TYR D 385 PHE 0.015 0.003 PHE D 298 TRP 0.014 0.004 TRP D 357 HIS 0.008 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.36 (17078) covalent geometry : angle 0.82131 / 0.42 (25918) hydrogen bonds : bond 0.08083 / 4.79 ( 702) hydrogen bonds : angle 3.62861 / 2.07 ( 1383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 35 time to evaluate : 0.278 Fit side-chains REVERT: D 16 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7767 (mt) REVERT: D 30 GLU cc_start: 0.2353 (OUTLIER) cc_final: 0.1942 (pm20) REVERT: D 63 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: D 96 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6593 (mp10) REVERT: D 117 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.5225 (mpt180) REVERT: D 206 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6847 (tpt) REVERT: D 236 MET cc_start: 0.5289 (ttt) cc_final: 0.4960 (ttt) REVERT: D 270 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7860 (tp) REVERT: D 300 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8014 (mptm) REVERT: D 347 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7323 (mmp-170) REVERT: D 358 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8527 (tptt) outliers start: 36 outliers final: 7 residues processed: 66 average time/residue: 0.6048 time to fit residues: 44.2501 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 2 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 0.0570 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.201118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155671 restraints weight = 20175.283| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 0.83 r_work: 0.3572 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17078 Z= 0.158 Angle : 0.659 8.341 25918 Z= 0.345 Chirality : 0.036 0.251 3318 Planarity : 0.006 0.139 1121 Dihedral : 19.188 178.361 7299 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.15 % Favored : 96.59 % Rotamer: Outliers : 6.74 % Allowed : 31.38 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.35 (0.41), residues: 381 helix: 0.78 (0.31), residues: 259 sheet: 0.86 (1.00), residues: 24 loop : -1.24 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 172 TYR 0.023 0.002 TYR D 385 PHE 0.009 0.002 PHE D 275 TRP 0.013 0.001 TRP D 357 HIS 0.002 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (17078) covalent geometry : angle 0.65917 / 0.35 (25918) hydrogen bonds : bond 0.06616 / 3.92 ( 702) hydrogen bonds : angle 3.32404 / 1.89 ( 1383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.302 Fit side-chains REVERT: D 63 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: D 96 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6560 (mp10) REVERT: D 216 LYS cc_start: 0.8320 (tttm) cc_final: 0.8105 (ttpm) REVERT: D 236 MET cc_start: 0.5020 (ttt) cc_final: 0.4637 (ttt) REVERT: D 270 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7673 (tp) REVERT: D 300 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7752 (mmmt) REVERT: D 358 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8491 (tptt) outliers start: 23 outliers final: 6 residues processed: 60 average time/residue: 0.6142 time to fit residues: 40.7983 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 151 HIS ** 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 = 0.4353 r_free = 0.4353 target = 0.198490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.154166 restraints weight = 20066.252| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 0.92 r_work: 0.3513 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 17078 Z= 0.241 Angle : 0.694 7.832 25918 Z= 0.363 Chirality : 0.039 0.264 3318 Planarity : 0.007 0.135 1121 Dihedral : 19.111 178.563 7297 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.67 % Favored : 96.06 % Rotamer: Outliers : 7.04 % Allowed : 29.91 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.29 (0.41), residues: 381 helix: 0.76 (0.31), residues: 256 sheet: 1.03 (1.03), residues: 24 loop : -1.35 (0.59), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 347 TYR 0.029 0.002 TYR D 385 PHE 0.011 0.002 PHE D 89 TRP 0.013 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.24 (17078) covalent geometry : angle 0.69357 / 0.36 (25918) hydrogen bonds : bond 0.06846 / 4.06 ( 702) hydrogen bonds : angle 3.30116 / 1.89 ( 1383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: D 35 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.6116 (ttm) REVERT: D 63 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: D 214 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6575 (mmt) REVERT: D 219 LEU cc_start: 0.7023 (mm) cc_final: 0.6622 (mt) REVERT: D 270 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7829 (tp) REVERT: D 300 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7957 (mptm) outliers start: 24 outliers final: 10 residues processed: 59 average time/residue: 0.5415 time to fit residues: 35.6452 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 chunk 43 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 150 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 = 0.4303 r_free = 0.4303 target = 0.194511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.150539 restraints weight = 19924.459| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.03 r_work: 0.3461 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 17078 Z= 0.300 Angle : 0.773 11.280 25918 Z= 0.401 Chirality : 0.042 0.259 3318 Planarity : 0.007 0.131 1121 Dihedral : 19.230 179.864 7297 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.20 % Favored : 95.54 % Rotamer: Outliers : 6.74 % Allowed : 30.21 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.40), residues: 381 helix: 0.31 (0.30), residues: 257 sheet: 0.84 (1.09), residues: 24 loop : -1.75 (0.55), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 172 TYR 0.035 0.003 TYR D 385 PHE 0.018 0.003 PHE D 275 TRP 0.013 0.003 TRP D 357 HIS 0.007 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.30 (17078) covalent geometry : angle 0.77265 / 0.40 (25918) hydrogen bonds : bond 0.07787 / 4.62 ( 702) hydrogen bonds : angle 3.46250 / 1.98 ( 1383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.263 Fit side-chains REVERT: D 35 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.6141 (ttm) REVERT: D 43 HIS cc_start: 0.5742 (OUTLIER) cc_final: 0.5539 (m90) REVERT: D 63 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: D 96 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6596 (mp10) REVERT: D 139 ASP cc_start: 0.7057 (t0) cc_final: 0.6618 (p0) REVERT: D 146 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6406 (t80) REVERT: D 219 LEU cc_start: 0.7038 (mm) cc_final: 0.6802 (mt) REVERT: D 270 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7826 (tp) REVERT: D 300 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.7945 (mptm) outliers start: 23 outliers final: 10 residues processed: 63 average time/residue: 0.5279 time to fit residues: 37.1683 Evaluate side-chains 61 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.196908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.151197 restraints weight = 19932.666| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.05 r_work: 0.3514 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 17078 Z= 0.261 Angle : 0.713 10.152 25918 Z= 0.371 Chirality : 0.040 0.245 3318 Planarity : 0.007 0.129 1121 Dihedral : 19.173 178.625 7297 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 5.28 % Allowed : 32.55 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.40), residues: 381 helix: 0.56 (0.30), residues: 256 sheet: 0.77 (1.11), residues: 24 loop : -1.75 (0.56), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 172 TYR 0.027 0.002 TYR D 385 PHE 0.012 0.003 PHE D 298 TRP 0.015 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.26 (17078) covalent geometry : angle 0.71251 / 0.37 (25918) hydrogen bonds : bond 0.07171 / 4.26 ( 702) hydrogen bonds : angle 3.34481 / 1.91 ( 1383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.208 Fit side-chains REVERT: D 35 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.6191 (ttm) REVERT: D 63 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: D 96 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6721 (mp10) REVERT: D 139 ASP cc_start: 0.6973 (t0) cc_final: 0.6682 (p0) REVERT: D 146 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6361 (t80) REVERT: D 214 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6366 (mmt) REVERT: D 219 LEU cc_start: 0.7001 (mm) cc_final: 0.6782 (mt) REVERT: D 231 MET cc_start: 0.7425 (mpp) cc_final: 0.7038 (mpp) REVERT: D 236 MET cc_start: 0.5264 (ttt) cc_final: 0.4799 (ttt) REVERT: D 270 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7788 (tp) REVERT: D 300 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7830 (mmmt) outliers start: 18 outliers final: 7 residues processed: 55 average time/residue: 0.5451 time to fit residues: 33.3973 Evaluate side-chains 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 37 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 0.0470 chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 150 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 = 0.4343 r_free = 0.4343 target = 0.197677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.153619 restraints weight = 20112.300| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 0.89 r_work: 0.3500 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17078 Z= 0.226 Angle : 0.681 11.143 25918 Z= 0.357 Chirality : 0.038 0.241 3318 Planarity : 0.006 0.126 1121 Dihedral : 19.105 178.443 7297 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Rotamer: Outliers : 4.40 % Allowed : 33.72 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.41), residues: 381 helix: 0.81 (0.31), residues: 256 sheet: 0.48 (1.12), residues: 24 loop : -1.67 (0.57), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 172 TYR 0.027 0.002 TYR D 385 PHE 0.009 0.002 PHE D 298 TRP 0.013 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.23 (17078) covalent geometry : angle 0.68136 / 0.36 (25918) hydrogen bonds : bond 0.06916 / 4.11 ( 702) hydrogen bonds : angle 3.28601 / 1.88 ( 1383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.267 Fit side-chains REVERT: D 35 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.6067 (ttm) REVERT: D 63 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: D 96 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6636 (mp10) REVERT: D 139 ASP cc_start: 0.6841 (t0) cc_final: 0.6639 (p0) REVERT: D 146 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6412 (t80) REVERT: D 152 ASP cc_start: 0.5648 (m-30) cc_final: 0.5044 (t0) REVERT: D 214 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6457 (mmt) REVERT: D 236 MET cc_start: 0.5299 (ttt) cc_final: 0.4859 (ttt) REVERT: D 270 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7802 (tp) REVERT: D 300 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7820 (mmmt) outliers start: 15 outliers final: 6 residues processed: 53 average time/residue: 0.5633 time to fit residues: 33.2826 Evaluate side-chains 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 23 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 43 HIS ** 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 = 0.4349 r_free = 0.4349 target = 0.198414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.153771 restraints weight = 20064.011| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.07 r_work: 0.3544 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17078 Z= 0.173 Angle : 0.662 11.626 25918 Z= 0.348 Chirality : 0.036 0.237 3318 Planarity : 0.007 0.124 1121 Dihedral : 19.098 178.083 7297 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.94 % Favored : 95.54 % Rotamer: Outliers : 4.69 % Allowed : 33.14 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.41), residues: 381 helix: 1.02 (0.31), residues: 256 sheet: 0.62 (1.13), residues: 24 loop : -1.59 (0.58), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 172 TYR 0.024 0.002 TYR D 385 PHE 0.011 0.002 PHE D 298 TRP 0.012 0.001 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (17078) covalent geometry : angle 0.66156 / 0.35 (25918) hydrogen bonds : bond 0.06769 / 4.03 ( 702) hydrogen bonds : angle 3.24108 / 1.86 ( 1383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: D 35 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.6078 (ttm) REVERT: D 63 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: D 146 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6462 (t80) REVERT: D 152 ASP cc_start: 0.5702 (m-30) cc_final: 0.5047 (t0) REVERT: D 214 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6352 (mmt) REVERT: D 236 MET cc_start: 0.5134 (ttt) cc_final: 0.4709 (ttt) REVERT: D 270 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7774 (tp) REVERT: D 300 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7725 (mmmt) outliers start: 16 outliers final: 8 residues processed: 52 average time/residue: 0.6052 time to fit residues: 34.8292 Evaluate side-chains 53 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 chunk 8 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 HIS ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.196279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152100 restraints weight = 20010.433| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.25 r_work: 0.3485 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 17078 Z= 0.295 Angle : 0.736 11.881 25918 Z= 0.383 Chirality : 0.041 0.257 3318 Planarity : 0.007 0.124 1121 Dihedral : 19.075 178.852 7297 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Rotamer: Outliers : 4.11 % Allowed : 34.02 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.41), residues: 381 helix: 0.80 (0.31), residues: 256 sheet: 0.45 (1.09), residues: 24 loop : -1.77 (0.55), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 172 TYR 0.031 0.002 TYR D 385 PHE 0.015 0.003 PHE D 298 TRP 0.013 0.003 TRP D 357 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.29 (17078) covalent geometry : angle 0.73551 / 0.38 (25918) hydrogen bonds : bond 0.07281 / 4.32 ( 702) hydrogen bonds : angle 3.30424 / 1.90 ( 1383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.276 Fit side-chains REVERT: D 35 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6141 (ttm) REVERT: D 63 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: D 96 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6550 (mp10) REVERT: D 146 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6477 (t80) REVERT: D 214 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6450 (mmt) REVERT: D 236 MET cc_start: 0.5285 (ttt) cc_final: 0.4835 (ttt) REVERT: D 270 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7798 (tp) REVERT: D 300 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7899 (mptm) outliers start: 14 outliers final: 6 residues processed: 47 average time/residue: 0.6460 time to fit residues: 33.5060 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.196236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153126 restraints weight = 19949.760| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.00 r_work: 0.3494 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17078 Z= 0.291 Angle : 0.732 11.037 25918 Z= 0.382 Chirality : 0.041 0.251 3318 Planarity : 0.007 0.123 1121 Dihedral : 19.096 179.220 7297 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.94 % Favored : 95.54 % Rotamer: Outliers : 4.11 % Allowed : 33.72 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.41), residues: 381 helix: 0.59 (0.30), residues: 262 sheet: 0.40 (1.06), residues: 24 loop : -1.65 (0.58), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 172 TYR 0.029 0.002 TYR D 385 PHE 0.014 0.003 PHE D 113 TRP 0.014 0.003 TRP D 357 HIS 0.005 0.002 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.29 (17078) covalent geometry : angle 0.73172 / 0.38 (25918) hydrogen bonds : bond 0.07338 / 4.36 ( 702) hydrogen bonds : angle 3.32862 / 1.91 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5754.21 seconds wall clock time: 98 minutes 45.43 seconds (5925.43 seconds total)