Starting phenix.real_space_refine on Wed Mar 4 18:09:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uin_26550/03_2026/7uin_26550.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uin_26550/03_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_26550/03_2026/7uin_26550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uin_26550/03_2026/7uin_26550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uin_26550/03_2026/7uin_26550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uin_26550/03_2026/7uin_26550.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.25, per 1000 atoms: 0.21 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: 1.28 Conformation dependent library (CDL) restraints added in 257.3 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: 2.60 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: 3.99 Time building geometry restraints manager: 1.73 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=" 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 bond pdb=" CA PRO D 281 " pdb=" CB PRO D 281 " ideal model delta sigma weight residual 1.534 1.462 0.072 1.40e-02 5.10e+03 2.63e+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: 9034 35.84 - 71.68: 1447 71.68 - 107.51: 157 107.51 - 143.35: 8 143.35 - 179.19: 10 Dihedral angle restraints: 10656 sinusoidal: 9532 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 10653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3113 0.087 - 0.175: 179 0.175 - 0.262: 14 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.900 Find NCS groups from input model: 0.040 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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= 0.357 Angle : 1.206 106.017 25918 Z= 0.554 Chirality : 0.047 0.437 3318 Planarity : 0.009 0.108 1121 Dihedral : 25.610 179.187 9932 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 covalent geometry : bond 0.01014 (17078) covalent geometry : angle 1.20608 (25918) hydrogen bonds : bond 0.12652 ( 702) hydrogen bonds : angle 5.82068 ( 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 : 0.298 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.6215 time to fit residues: 40.3955 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 : 0.172 ------------------------------------------------------------------------------- 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: 10.0000 chunk 74 optimal weight: 0.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.200460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155406 restraints weight = 20087.636| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 0.86 r_work: 0.3573 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 17078 Z= 0.220 Angle : 0.695 7.198 25918 Z= 0.360 Chirality : 0.037 0.284 3318 Planarity : 0.007 0.139 1121 Dihedral : 25.528 177.479 9140 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.15 % Favored : 96.33 % Rotamer: Outliers : 8.50 % Allowed : 31.38 % Favored : 60.12 % 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: 0.08 (0.40), residues: 381 helix: 0.44 (0.29), residues: 258 sheet: 0.38 (0.94), residues: 24 loop : -0.77 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 282 TYR 0.028 0.002 TYR D 385 PHE 0.018 0.002 PHE D 298 TRP 0.011 0.002 TRP D 357 HIS 0.003 0.001 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00434 (17078) covalent geometry : angle 0.69530 (25918) hydrogen bonds : bond 0.06679 ( 702) hydrogen bonds : angle 3.42764 ( 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 70 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: D 63 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: D 167 VAL cc_start: 0.5809 (t) cc_final: 0.5323 (p) REVERT: D 236 MET cc_start: 0.5097 (OUTLIER) cc_final: 0.4732 (ttt) REVERT: D 270 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7540 (tp) REVERT: D 300 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7839 (mmmt) REVERT: D 358 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8472 (tptp) outliers start: 29 outliers final: 3 residues processed: 66 average time/residue: 0.6390 time to fit residues: 46.2836 Evaluate side-chains 45 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 161 THR Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 55 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4296 r_free = 0.4296 target = 0.194183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.149855 restraints weight = 20209.945| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.02 r_work: 0.3454 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 17078 Z= 0.325 Angle : 0.786 7.723 25918 Z= 0.404 Chirality : 0.043 0.265 3318 Planarity : 0.008 0.136 1121 Dihedral : 25.565 178.127 9131 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 9.38 % Allowed : 28.45 % 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: -0.11 (0.40), residues: 381 helix: 0.34 (0.30), residues: 257 sheet: 1.10 (1.01), residues: 24 loop : -1.24 (0.59), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 88 TYR 0.033 0.003 TYR D 385 PHE 0.018 0.003 PHE D 298 TRP 0.013 0.003 TRP D 357 HIS 0.006 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00641 (17078) covalent geometry : angle 0.78605 (25918) hydrogen bonds : bond 0.07964 ( 702) hydrogen bonds : angle 3.52269 ( 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 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 46 time to evaluate : 0.258 Fit side-chains REVERT: D 30 GLU cc_start: 0.2093 (OUTLIER) cc_final: 0.1849 (pm20) REVERT: D 63 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: D 117 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.5242 (mpt180) REVERT: D 167 VAL cc_start: 0.6155 (t) cc_final: 0.5768 (p) REVERT: D 219 LEU cc_start: 0.7182 (mm) cc_final: 0.6947 (mt) REVERT: D 270 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7775 (tp) REVERT: D 300 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7967 (mptm) outliers start: 32 outliers final: 7 residues processed: 72 average time/residue: 0.5614 time to fit residues: 44.7049 Evaluate side-chains 52 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 63 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 2 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.195678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.149893 restraints weight = 20011.402| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 0.95 r_work: 0.3484 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 17078 Z= 0.291 Angle : 0.730 9.383 25918 Z= 0.376 Chirality : 0.040 0.249 3318 Planarity : 0.008 0.130 1121 Dihedral : 25.438 178.746 9128 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 7.33 % Allowed : 31.38 % Favored : 61.29 % 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: 0.58 (0.31), residues: 256 sheet: 0.74 (1.01), residues: 24 loop : -1.48 (0.57), 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 0.014 0.003 PHE D 298 TRP 0.014 0.003 TRP D 357 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00572 (17078) covalent geometry : angle 0.72970 (25918) hydrogen bonds : bond 0.07263 ( 702) hydrogen bonds : angle 3.36133 ( 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 70 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.248 Fit side-chains REVERT: D 63 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: D 96 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6590 (mp10) REVERT: D 117 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.5318 (mpt180) REVERT: D 146 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6451 (t80) REVERT: D 167 VAL cc_start: 0.6327 (t) cc_final: 0.6042 (p) REVERT: D 270 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7788 (tp) REVERT: D 300 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7906 (mptm) REVERT: D 343 GLU cc_start: 0.7460 (tp30) cc_final: 0.7253 (tt0) outliers start: 25 outliers final: 7 residues processed: 65 average time/residue: 0.5992 time to fit residues: 42.8027 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain D residue 117 ARG 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 50 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 30.0000 chunk 56 optimal weight: 0.0050 chunk 85 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.201518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155230 restraints weight = 20364.829| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 0.76 r_work: 0.3598 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2858 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= 0.154 Angle : 0.626 7.548 25918 Z= 0.326 Chirality : 0.034 0.230 3318 Planarity : 0.006 0.127 1121 Dihedral : 25.270 179.378 9127 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 5.28 % Allowed : 31.38 % Favored : 63.34 % 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: 0.73 (0.42), residues: 381 helix: 1.11 (0.31), residues: 262 sheet: 0.77 (1.00), residues: 24 loop : -1.24 (0.62), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 347 TYR 0.016 0.002 TYR D 385 PHE 0.009 0.002 PHE D 89 TRP 0.010 0.001 TRP D 357 HIS 0.003 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00300 (17078) covalent geometry : angle 0.62593 (25918) hydrogen bonds : bond 0.06120 ( 702) hydrogen bonds : angle 3.09713 ( 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 64 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: D 35 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.6090 (ttm) REVERT: D 63 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: D 146 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6399 (t80) REVERT: D 167 VAL cc_start: 0.6215 (t) cc_final: 0.5943 (p) REVERT: D 214 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6318 (mmt) REVERT: D 253 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8157 (mt) REVERT: D 300 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7694 (mmmt) outliers start: 18 outliers final: 6 residues processed: 56 average time/residue: 0.5816 time to fit residues: 36.1472 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 103 GLU 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 253 LEU Chi-restraints excluded: chain D residue 255 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: 1.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.196739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.153151 restraints weight = 19951.848| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 0.93 r_work: 0.3507 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17078 Z= 0.267 Angle : 0.704 8.693 25918 Z= 0.364 Chirality : 0.039 0.248 3318 Planarity : 0.006 0.123 1121 Dihedral : 25.301 179.047 9127 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Rotamer: Outliers : 5.57 % Allowed : 30.21 % Favored : 64.22 % 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: 0.55 (0.41), residues: 381 helix: 0.98 (0.31), residues: 263 sheet: 0.93 (1.02), residues: 24 loop : -1.41 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 382 TYR 0.030 0.002 TYR D 385 PHE 0.013 0.002 PHE D 298 TRP 0.011 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00524 (17078) covalent geometry : angle 0.70352 (25918) hydrogen bonds : bond 0.07089 ( 702) hydrogen bonds : angle 3.18432 ( 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 61 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: D 35 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.6104 (ttm) REVERT: D 146 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.6533 (t80) REVERT: D 167 VAL cc_start: 0.6401 (t) cc_final: 0.6144 (p) REVERT: D 300 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7821 (mmmt) outliers start: 19 outliers final: 8 residues processed: 56 average time/residue: 0.5570 time to fit residues: 34.6632 Evaluate side-chains 51 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 103 GLU 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 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: 0.0050 chunk 72 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 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: 4.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4346 r_free = 0.4346 target = 0.197920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.154687 restraints weight = 19967.726| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 0.83 r_work: 0.3538 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17078 Z= 0.211 Angle : 0.665 9.011 25918 Z= 0.347 Chirality : 0.036 0.231 3318 Planarity : 0.006 0.127 1121 Dihedral : 25.296 178.875 9127 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.20 % Favored : 95.54 % Rotamer: Outliers : 5.57 % Allowed : 30.79 % Favored : 63.64 % 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: 0.65 (0.42), residues: 381 helix: 1.06 (0.31), residues: 263 sheet: 0.89 (1.03), residues: 24 loop : -1.37 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 407 TYR 0.026 0.002 TYR D 385 PHE 0.012 0.002 PHE D 298 TRP 0.012 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00411 (17078) covalent geometry : angle 0.66528 (25918) hydrogen bonds : bond 0.06847 ( 702) hydrogen bonds : angle 3.14002 ( 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: 19 poor density : 42 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: D 7 MET cc_start: 0.5858 (mmm) cc_final: 0.5410 (tpp) REVERT: D 35 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.6082 (ttm) REVERT: D 146 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6538 (t80) REVERT: D 270 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7777 (tp) REVERT: D 300 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7811 (mmmt) outliers start: 19 outliers final: 10 residues processed: 55 average time/residue: 0.5768 time to fit residues: 35.2442 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 213 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 37 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 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 = 0.4320 r_free = 0.4320 target = 0.195631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.152083 restraints weight = 20073.879| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 0.98 r_work: 0.3482 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 17078 Z= 0.298 Angle : 0.741 8.446 25918 Z= 0.382 Chirality : 0.041 0.254 3318 Planarity : 0.007 0.125 1121 Dihedral : 25.376 179.985 9127 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.46 % Favored : 95.28 % Rotamer: Outliers : 5.28 % Allowed : 31.38 % Favored : 63.34 % 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: 0.31 (0.42), residues: 381 helix: 0.80 (0.31), residues: 263 sheet: 0.80 (1.03), residues: 24 loop : -1.50 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 88 TYR 0.031 0.002 TYR D 385 PHE 0.014 0.003 PHE D 298 TRP 0.012 0.002 TRP D 357 HIS 0.005 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00583 (17078) covalent geometry : angle 0.74082 (25918) hydrogen bonds : bond 0.07559 ( 702) hydrogen bonds : angle 3.24237 ( 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: 18 poor density : 40 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.6129 (ttm) REVERT: D 146 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6578 (t80) REVERT: D 259 MET cc_start: 0.7436 (tpt) cc_final: 0.7219 (tmt) REVERT: D 270 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7851 (tp) REVERT: D 300 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7942 (mptm) outliers start: 18 outliers final: 13 residues processed: 52 average time/residue: 0.5885 time to fit residues: 33.7942 Evaluate side-chains 56 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 213 GLU 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 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 256 LYS 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: 3.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 284 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 = 0.4387 r_free = 0.4387 target = 0.202217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.157470 restraints weight = 20372.756| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 0.69 r_work: 0.3604 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17078 Z= 0.143 Angle : 0.610 9.484 25918 Z= 0.317 Chirality : 0.033 0.231 3318 Planarity : 0.006 0.123 1121 Dihedral : 25.170 179.760 9127 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.67 % Favored : 96.06 % Rotamer: Outliers : 4.69 % Allowed : 32.55 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.43), residues: 381 helix: 1.40 (0.32), residues: 263 sheet: 0.69 (1.01), residues: 24 loop : -1.37 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 382 TYR 0.017 0.001 TYR D 385 PHE 0.009 0.002 PHE D 298 TRP 0.013 0.002 TRP D 357 HIS 0.001 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00277 (17078) covalent geometry : angle 0.61003 (25918) hydrogen bonds : bond 0.05920 ( 702) hydrogen bonds : angle 2.99399 ( 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 : 0.302 Fit side-chains revert: symmetry clash REVERT: D 35 MET cc_start: 0.6447 (OUTLIER) cc_final: 0.6197 (ttm) REVERT: D 146 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6519 (t80) REVERT: D 259 MET cc_start: 0.7468 (tpt) cc_final: 0.7267 (tmt) REVERT: D 270 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7729 (tp) REVERT: D 300 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7688 (mmmt) outliers start: 16 outliers final: 7 residues processed: 52 average time/residue: 0.4789 time to fit residues: 28.1585 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 : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 146 PHE 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: 0.9990 chunk 57 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 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 = 0.4309 r_free = 0.4309 target = 0.194465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155987 restraints weight = 20054.266| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.34 r_work: 0.3445 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 17078 Z= 0.378 Angle : 0.809 10.699 25918 Z= 0.412 Chirality : 0.045 0.278 3318 Planarity : 0.007 0.121 1121 Dihedral : 25.373 179.088 9127 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.46 % Favored : 95.28 % Rotamer: Outliers : 5.28 % Allowed : 31.67 % 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: 0.12 (0.42), residues: 381 helix: 0.68 (0.31), residues: 262 sheet: 0.60 (1.02), residues: 24 loop : -1.61 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 347 TYR 0.034 0.003 TYR D 385 PHE 0.019 0.003 PHE D 298 TRP 0.012 0.003 TRP D 357 HIS 0.006 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00739 (17078) covalent geometry : angle 0.80885 (25918) hydrogen bonds : bond 0.08200 ( 702) hydrogen bonds : angle 3.30377 ( 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 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: D 146 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6647 (t80) REVERT: D 214 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6200 (mmt) REVERT: D 270 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7788 (tp) REVERT: D 300 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7988 (mptm) outliers start: 18 outliers final: 9 residues processed: 48 average time/residue: 0.6019 time to fit residues: 32.0255 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 213 GLU 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: 2.9990 chunk 94 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 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 = 0.4357 r_free = 0.4357 target = 0.199020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.156053 restraints weight = 20033.094| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 0.81 r_work: 0.3553 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17078 Z= 0.193 Angle : 0.645 10.516 25918 Z= 0.335 Chirality : 0.035 0.232 3318 Planarity : 0.006 0.121 1121 Dihedral : 25.220 179.917 9127 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.15 % Favored : 96.33 % Rotamer: Outliers : 4.40 % Allowed : 32.55 % Favored : 63.05 % 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: 0.56 (0.42), residues: 381 helix: 1.04 (0.31), residues: 262 sheet: 0.49 (1.02), residues: 24 loop : -1.45 (0.61), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 172 TYR 0.024 0.002 TYR D 385 PHE 0.012 0.002 PHE D 298 TRP 0.012 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00377 (17078) covalent geometry : angle 0.64508 (25918) hydrogen bonds : bond 0.06450 ( 702) hydrogen bonds : angle 3.08461 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5507.53 seconds wall clock time: 94 minutes 24.16 seconds (5664.16 seconds total)