Starting phenix.real_space_refine on Sat Sep 12 10:55:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uin_26550/09_2026/7uin_26550.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uin_26550/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7uin_26550/09_2026/7uin_26550.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uin_26550/09_2026/7uin_26550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uin_26550/09_2026/7uin_26550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uin_26550/09_2026/7uin_26550.map" model { file = "/net/cci-nas-00/data/ceres_data/7uin_26550/09_2026/7uin_26550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uin_26550/09_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: 3.18, per 1000 atoms: 0.20 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: 1.18 Conformation dependent library (CDL) restraints added in 303.0 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: 2.63 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: 4.09 Time building geometry restraints manager: 1.64 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=" C3' A B 204 " pdb=" O3' A B 204 " pdb=" P A B 205 " ideal model delta sigma weight residual 119.70 128.62 -8.92 1.20e+00 6.94e-01 5.53e+01 ... (remaining 25913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 7563 35.84 - 71.68: 1204 71.68 - 107.51: 48 107.51 - 143.35: 4 143.35 - 179.19: 7 Dihedral angle restraints: 8826 sinusoidal: 7702 harmonic: 1124 Sorted by residual: dihedral pdb=" C4' A B 426 " pdb=" C3' A B 426 " pdb=" C2' A B 426 " pdb=" C1' A B 426 " ideal model delta sinusoidal sigma weight residual 36.34 -43.27 79.62 1 3.10e+00 1.04e-01 8.19e+02 dihedral pdb=" C4' A B 339 " pdb=" C3' A B 339 " pdb=" C2' A B 339 " pdb=" C1' A B 339 " ideal model delta sinusoidal sigma weight residual 36.35 -38.31 74.66 1 3.10e+00 1.04e-01 7.35e+02 dihedral pdb=" C4' U B 593 " pdb=" C3' U B 593 " pdb=" C2' U B 593 " pdb=" C1' U B 593 " ideal model delta sinusoidal sigma weight residual 36.34 -38.24 74.59 1 3.10e+00 1.04e-01 7.34e+02 ... (remaining 8823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2493 0.087 - 0.175: 187 0.175 - 0.262: 533 0.262 - 0.350: 91 0.350 - 0.437: 14 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=" C2' A B 426 " pdb=" C3' A B 426 " pdb=" O2' A B 426 " pdb=" C1' A B 426 " both_signs ideal model delta sigma weight residual False -2.79 -2.38 -0.41 2.00e-01 2.50e+01 4.10e+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: 3.910 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: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.880 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- 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= 0.410 Angle : 1.400 106.017 25918 Z= 0.621 Chirality : 0.113 0.437 3318 Planarity : 0.009 0.108 1121 Dihedral : 23.512 179.187 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 0.01043 / 0.41 (17078) covalent geometry : angle 1.39958 / 0.62 (25918) hydrogen bonds : bond 0.12652 / 6.58 ( 702) hydrogen bonds : angle 5.82068 / 2.37 ( 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 : 0.259 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.6242 time to fit residues: 40.7591 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 : 0.253 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.203018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161487 restraints weight = 20513.322| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 0.74 r_work: 0.3616 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 17078 Z= 0.273 Angle : 1.471 19.183 25918 Z= 0.605 Chirality : 0.129 1.807 3318 Planarity : 0.007 0.141 1121 Dihedral : 21.282 178.262 7310 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.89 % Favored : 96.59 % Rotamer: Outliers : 6.74 % Allowed : 33.43 % Favored : 59.82 % 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: -0.13 (0.40), residues: 381 helix: 0.23 (0.30), residues: 258 sheet: 0.29 (0.97), residues: 24 loop : -0.71 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 389 TYR 0.026 0.002 TYR D 385 PHE 0.017 0.003 PHE D 298 TRP 0.010 0.002 TRP D 357 HIS 0.004 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.27 (17078) covalent geometry : angle 1.47111 / 0.61 (25918) hydrogen bonds : bond 0.07495 / 3.85 ( 702) hydrogen bonds : angle 3.63545 / 1.43 ( 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 62 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.279 Fit side-chains REVERT: D 63 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: D 117 ARG cc_start: 0.7323 (mmt90) cc_final: 0.7070 (mtt180) REVERT: D 300 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7966 (mmmt) REVERT: D 358 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8568 (tptt) outliers start: 23 outliers final: 7 residues processed: 57 average time/residue: 0.6249 time to fit residues: 39.1482 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 : 0.270 ------------------------------------------------------------------------------- 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 358 LYS Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 415 SER 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: 7.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.198115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159817 restraints weight = 20293.501| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.15 r_work: 0.3513 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 17078 Z= 0.375 Angle : 1.361 14.958 25918 Z= 0.562 Chirality : 0.105 1.116 3318 Planarity : 0.007 0.142 1121 Dihedral : 21.147 179.369 7302 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 9.09 % Allowed : 29.91 % Favored : 61.00 % 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: -0.26 (0.41), residues: 381 helix: 0.24 (0.31), residues: 253 sheet: 1.04 (0.97), residues: 24 loop : -1.27 (0.59), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 389 TYR 0.037 0.004 TYR D 385 PHE 0.018 0.003 PHE D 298 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 0.00761 / 0.38 (17078) covalent geometry : angle 1.36093 / 0.56 (25918) hydrogen bonds : bond 0.08548 / 4.41 ( 702) hydrogen bonds : angle 3.58658 / 1.40 ( 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: 31 poor density : 40 time to evaluate : 0.182 Fit side-chains REVERT: D 16 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7802 (mt) REVERT: D 30 GLU cc_start: 0.2154 (OUTLIER) cc_final: 0.1906 (pm20) REVERT: D 63 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: D 96 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6552 (mp10) REVERT: D 236 MET cc_start: 0.5549 (ttt) cc_final: 0.5206 (ttt) REVERT: D 270 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7789 (tp) REVERT: D 300 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8037 (mptm) REVERT: D 347 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7225 (mmp-170) REVERT: D 358 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8515 (tptt) outliers start: 31 outliers final: 6 residues processed: 67 average time/residue: 0.6271 time to fit residues: 46.1429 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 92 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.200690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.159350 restraints weight = 20306.055| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 0.77 r_work: 0.3593 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2645 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= 0.276 Angle : 1.195 13.625 25918 Z= 0.494 Chirality : 0.091 0.967 3318 Planarity : 0.007 0.139 1121 Dihedral : 21.091 178.559 7299 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.94 % Favored : 95.80 % Rotamer: Outliers : 8.50 % Allowed : 30.50 % Favored : 61.00 % 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: -0.03 (0.41), residues: 381 helix: 0.43 (0.30), residues: 256 sheet: 0.99 (0.99), residues: 24 loop : -1.22 (0.62), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 326 TYR 0.026 0.003 TYR D 385 PHE 0.011 0.002 PHE D 298 TRP 0.014 0.002 TRP D 357 HIS 0.005 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.28 (17078) covalent geometry : angle 1.19542 / 0.49 (25918) hydrogen bonds : bond 0.07486 / 3.86 ( 702) hydrogen bonds : angle 3.40439 / 1.32 ( 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 67 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 38 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: D 63 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: D 236 MET cc_start: 0.5472 (ttt) cc_final: 0.5093 (ttt) REVERT: D 270 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7715 (tp) REVERT: D 300 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7994 (mptm) outliers start: 29 outliers final: 8 residues processed: 62 average time/residue: 0.5686 time to fit residues: 39.1207 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 161 THR Chi-restraints excluded: chain D residue 199 SER 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=3.50 ------------------------------------------------------------------------------- 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: 20.0000 chunk 56 optimal weight: 0.0770 chunk 85 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 overall best weight: 1.8144 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.199098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155069 restraints weight = 20377.708| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 0.81 r_work: 0.3546 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2882 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= 0.266 Angle : 1.169 13.560 25918 Z= 0.484 Chirality : 0.088 0.940 3318 Planarity : 0.007 0.135 1121 Dihedral : 21.035 178.317 7298 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.94 % Favored : 95.54 % Rotamer: Outliers : 5.28 % Allowed : 32.26 % Favored : 62.46 % 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: 0.21 (0.41), residues: 381 helix: 0.67 (0.31), residues: 256 sheet: 0.89 (1.01), residues: 24 loop : -1.24 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 217 TYR 0.028 0.002 TYR D 385 PHE 0.011 0.002 PHE D 298 TRP 0.011 0.002 TRP D 357 HIS 0.004 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.27 (17078) covalent geometry : angle 1.16934 / 0.48 (25918) hydrogen bonds : bond 0.07373 / 3.79 ( 702) hydrogen bonds : angle 3.33282 / 1.30 ( 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 60 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.200 Fit side-chains REVERT: D 35 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.6067 (ttm) REVERT: D 63 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: D 96 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6512 (mp10) REVERT: D 101 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7094 (tp) REVERT: D 139 ASP cc_start: 0.6955 (t0) cc_final: 0.6488 (p0) REVERT: D 219 LEU cc_start: 0.7056 (mm) cc_final: 0.6772 (mt) REVERT: D 236 MET cc_start: 0.5330 (ttt) cc_final: 0.4940 (ttt) REVERT: D 270 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7780 (tp) REVERT: D 300 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7741 (mmmt) outliers start: 18 outliers final: 3 residues processed: 56 average time/residue: 0.5953 time to fit residues: 37.0538 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 101 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.200684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158918 restraints weight = 20264.972| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 0.75 r_work: 0.3582 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 17078 Z= 0.227 Angle : 1.119 13.289 25918 Z= 0.462 Chirality : 0.084 0.864 3318 Planarity : 0.006 0.132 1121 Dihedral : 21.015 178.025 7297 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Rotamer: Outliers : 3.81 % Allowed : 32.55 % 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: 0.38 (0.41), residues: 381 helix: 0.86 (0.30), residues: 256 sheet: 0.94 (1.01), residues: 24 loop : -1.36 (0.59), 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 0.012 0.002 PHE D 275 TRP 0.012 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.23 (17078) covalent geometry : angle 1.11855 / 0.46 (25918) hydrogen bonds : bond 0.07130 / 3.66 ( 702) hydrogen bonds : angle 3.26465 / 1.26 ( 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 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: D 35 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.6095 (ttm) REVERT: D 63 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: D 139 ASP cc_start: 0.6903 (t0) cc_final: 0.6616 (p0) REVERT: D 152 ASP cc_start: 0.5702 (m-30) cc_final: 0.5168 (t0) REVERT: D 219 LEU cc_start: 0.7090 (mm) cc_final: 0.6857 (mt) REVERT: D 236 MET cc_start: 0.5333 (ttt) cc_final: 0.4928 (ttt) REVERT: D 270 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7720 (tp) REVERT: D 300 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7776 (mmmt) outliers start: 13 outliers final: 4 residues processed: 54 average time/residue: 0.5734 time to fit residues: 34.6440 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 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 300 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.198210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.156046 restraints weight = 20109.037| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 0.77 r_work: 0.3542 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 17078 Z= 0.290 Angle : 1.180 12.862 25918 Z= 0.488 Chirality : 0.088 0.925 3318 Planarity : 0.007 0.129 1121 Dihedral : 20.951 178.116 7297 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Rotamer: Outliers : 4.99 % Allowed : 32.55 % Favored : 62.46 % 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: 0.28 (0.41), residues: 381 helix: 0.83 (0.30), residues: 256 sheet: 0.72 (1.02), residues: 24 loop : -1.53 (0.57), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 217 TYR 0.031 0.002 TYR D 385 PHE 0.014 0.002 PHE D 298 TRP 0.012 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.29 (17078) covalent geometry : angle 1.18044 / 0.49 (25918) hydrogen bonds : bond 0.07508 / 3.85 ( 702) hydrogen bonds : angle 3.27441 / 1.26 ( 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 58 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: D 35 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.6146 (ttm) REVERT: D 63 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: D 146 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6213 (t80) REVERT: D 152 ASP cc_start: 0.5714 (m-30) cc_final: 0.5174 (t0) REVERT: D 214 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6165 (mmt) REVERT: D 219 LEU cc_start: 0.7014 (mm) cc_final: 0.6793 (mt) REVERT: D 236 MET cc_start: 0.5473 (ttt) cc_final: 0.5067 (ttt) REVERT: D 270 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7766 (tp) REVERT: D 300 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7948 (mptm) outliers start: 17 outliers final: 8 residues processed: 52 average time/residue: 0.6398 time to fit residues: 36.8234 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 : 0.291 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 37 optimal weight: 10.0000 chunk 75 optimal weight: 0.0870 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 90 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 overall best weight: 1.3120 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.200356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.158714 restraints weight = 20351.704| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 0.74 r_work: 0.3577 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17078 Z= 0.216 Angle : 1.126 13.550 25918 Z= 0.466 Chirality : 0.084 0.875 3318 Planarity : 0.006 0.126 1121 Dihedral : 20.985 177.722 7297 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 4.40 % Allowed : 33.43 % 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: 0.55 (0.41), residues: 381 helix: 1.08 (0.31), residues: 256 sheet: 0.76 (1.02), residues: 24 loop : -1.50 (0.58), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 172 TYR 0.024 0.002 TYR D 385 PHE 0.010 0.002 PHE D 298 TRP 0.012 0.002 TRP D 357 HIS 0.004 0.001 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.22 (17078) covalent geometry : angle 1.12550 / 0.47 (25918) hydrogen bonds : bond 0.07265 / 3.73 ( 702) hydrogen bonds : angle 3.20947 / 1.24 ( 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 56 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: D 35 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6138 (ttm) REVERT: D 43 HIS cc_start: 0.5624 (OUTLIER) cc_final: 0.5410 (m90) REVERT: D 63 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: D 152 ASP cc_start: 0.5677 (m-30) cc_final: 0.5169 (t0) REVERT: D 214 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6110 (mmt) REVERT: D 236 MET cc_start: 0.5287 (ttt) cc_final: 0.4883 (ttt) REVERT: D 270 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7659 (tp) REVERT: D 300 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7769 (mmmt) outliers start: 15 outliers final: 6 residues processed: 52 average time/residue: 0.5219 time to fit residues: 30.6264 Evaluate side-chains 51 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 241 VAL 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: 3.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 0.0020 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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 = 0.4361 r_free = 0.4361 target = 0.200564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158899 restraints weight = 20260.805| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 0.74 r_work: 0.3583 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17078 Z= 0.222 Angle : 1.114 12.838 25918 Z= 0.460 Chirality : 0.083 0.828 3318 Planarity : 0.006 0.125 1121 Dihedral : 20.933 177.367 7297 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Rotamer: Outliers : 4.11 % Allowed : 32.84 % 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: 0.71 (0.41), residues: 381 helix: 1.21 (0.31), residues: 256 sheet: 0.72 (1.00), residues: 24 loop : -1.47 (0.58), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 172 TYR 0.025 0.002 TYR D 385 PHE 0.010 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/Z covalent geometry : bond 0.00448 / 0.22 (17078) covalent geometry : angle 1.11355 / 0.46 (25918) hydrogen bonds : bond 0.07113 / 3.65 ( 702) hydrogen bonds : angle 3.15621 / 1.21 ( 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 52 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: D 16 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7910 (mt) REVERT: D 43 HIS cc_start: 0.5571 (OUTLIER) cc_final: 0.5369 (m90) REVERT: D 63 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: D 152 ASP cc_start: 0.5613 (m-30) cc_final: 0.5168 (t0) REVERT: D 214 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6317 (mmt) REVERT: D 236 MET cc_start: 0.5436 (ttt) cc_final: 0.5043 (ttt) REVERT: D 270 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7688 (tp) REVERT: D 300 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7838 (mmmt) outliers start: 14 outliers final: 6 residues processed: 48 average time/residue: 0.5566 time to fit residues: 29.8865 Evaluate side-chains 51 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU 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 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 241 VAL 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: 3.9990 chunk 4 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 HIS ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.195017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.152372 restraints weight = 20216.339| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 0.97 r_work: 0.3470 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 17078 Z= 0.411 Angle : 1.313 13.101 25918 Z= 0.542 Chirality : 0.096 1.028 3318 Planarity : 0.007 0.125 1121 Dihedral : 20.947 179.308 7297 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % 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: 0.09 (0.41), residues: 381 helix: 0.70 (0.31), residues: 256 sheet: 0.56 (1.04), residues: 24 loop : -1.59 (0.56), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 172 TYR 0.036 0.003 TYR D 385 PHE 0.019 0.003 PHE D 298 TRP 0.012 0.004 TRP D 357 HIS 0.005 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00839 / 0.41 (17078) covalent geometry : angle 1.31314 / 0.54 (25918) hydrogen bonds : bond 0.08434 / 4.32 ( 702) hydrogen bonds : angle 3.39375 / 1.31 ( 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 51 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.264 Fit side-chains REVERT: D 63 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: D 96 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: D 152 ASP cc_start: 0.5785 (m-30) cc_final: 0.5171 (t0) REVERT: D 214 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.5981 (mmt) REVERT: D 236 MET cc_start: 0.5266 (ttt) cc_final: 0.4920 (ttt) REVERT: D 270 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7820 (tp) REVERT: D 300 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7985 (mptm) outliers start: 14 outliers final: 7 residues processed: 48 average time/residue: 0.5631 time to fit residues: 30.1619 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 241 VAL 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: 0.9990 chunk 94 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.199550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.157300 restraints weight = 20249.689| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 0.73 r_work: 0.3566 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17078 Z= 0.234 Angle : 1.141 12.814 25918 Z= 0.471 Chirality : 0.085 0.894 3318 Planarity : 0.006 0.124 1121 Dihedral : 20.956 177.763 7297 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 3.23 % Allowed : 34.31 % Favored : 62.46 % 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: 0.54 (0.41), residues: 381 helix: 1.02 (0.31), residues: 258 sheet: 0.77 (1.04), residues: 24 loop : -1.42 (0.58), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 172 TYR 0.023 0.002 TYR D 385 PHE 0.012 0.002 PHE D 113 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 0.00474 / 0.23 (17078) covalent geometry : angle 1.14056 / 0.47 (25918) hydrogen bonds : bond 0.07308 / 3.75 ( 702) hydrogen bonds : angle 3.21706 / 1.24 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5365.48 seconds wall clock time: 92 minutes 10.53 seconds (5530.53 seconds total)