Starting phenix.real_space_refine on Sat May 2 16:28:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jl3_61577/05_2026/9jl3_61577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jl3_61577/05_2026/9jl3_61577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jl3_61577/05_2026/9jl3_61577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jl3_61577/05_2026/9jl3_61577.map" model { file = "/net/cci-nas-00/data/ceres_data/9jl3_61577/05_2026/9jl3_61577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jl3_61577/05_2026/9jl3_61577.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 177 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 3934 2.51 5 N 1285 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7274 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3507 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 411} Chain: "B" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3766 Classifications: {'DNA': 5, 'RNA': 172} Modifications used: {'rna2p_pur': 21, 'rna2p_pyr': 16, 'rna3p_pur': 68, 'rna3p_pyr': 67} Link IDs: {'rna2p': 37, 'rna3p': 139} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.10, per 1000 atoms: 0.29 Number of scatterers: 7274 At special positions: 0 Unit cell: (79.9, 130.05, 118.15, 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 13 16.00 P 177 15.00 Mg 1 11.99 O 1864 8.00 N 1285 7.00 C 3934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 310.9 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 56.2% alpha, 12.9% beta 58 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.626A pdb=" N ILE A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 101 removed outlier: 3.872A pdb=" N HIS A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.521A pdb=" N GLU A 105 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 144 through 148 removed outlier: 4.190A pdb=" N LEU A 148 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.565A pdb=" N LEU A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.917A pdb=" N LYS A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 336 through 368 removed outlier: 3.714A pdb=" N LEU A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 391 through 404 Processing helix chain 'A' and resid 405 through 413 removed outlier: 4.077A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 74 removed outlier: 3.504A pdb=" N LYS A 53 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 265 removed outlier: 3.668A pdb=" N GLU A 304 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 323 190 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 254 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1473 1.33 - 1.45: 2766 1.45 - 1.58: 3178 1.58 - 1.70: 349 1.70 - 1.82: 22 Bond restraints: 7788 Sorted by residual: bond pdb=" C CYS A 268 " pdb=" N ASP A 269 " ideal model delta sigma weight residual 1.332 1.443 -0.111 1.40e-02 5.10e+03 6.23e+01 bond pdb=" C PRO A 199 " pdb=" N LYS A 200 " ideal model delta sigma weight residual 1.331 1.256 0.075 1.48e-02 4.57e+03 2.53e+01 bond pdb=" C ASP A 269 " pdb=" N ASP A 270 " ideal model delta sigma weight residual 1.334 1.259 0.075 1.58e-02 4.01e+03 2.28e+01 bond pdb=" C ARG A 10 " pdb=" N LYS A 11 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.31e-02 5.83e+03 6.60e+00 bond pdb=" C PHE A 9 " pdb=" N ARG A 10 " ideal model delta sigma weight residual 1.332 1.304 0.028 1.25e-02 6.40e+03 4.85e+00 ... (remaining 7783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 11126 2.38 - 4.75: 193 4.75 - 7.13: 25 7.13 - 9.51: 1 9.51 - 11.88: 2 Bond angle restraints: 11347 Sorted by residual: angle pdb=" CA CYS A 268 " pdb=" C CYS A 268 " pdb=" N ASP A 269 " ideal model delta sigma weight residual 116.45 110.07 6.38 1.23e+00 6.61e-01 2.69e+01 angle pdb=" O CYS A 268 " pdb=" C CYS A 268 " pdb=" N ASP A 269 " ideal model delta sigma weight residual 123.27 128.97 -5.70 1.17e+00 7.31e-01 2.38e+01 angle pdb=" C TYR A 267 " pdb=" CA TYR A 267 " pdb=" CB TYR A 267 " ideal model delta sigma weight residual 117.23 110.82 6.41 1.36e+00 5.41e-01 2.22e+01 angle pdb=" O PRO A 199 " pdb=" C PRO A 199 " pdb=" N LYS A 200 " ideal model delta sigma weight residual 122.23 117.37 4.86 1.20e+00 6.94e-01 1.64e+01 angle pdb=" CB MET A 253 " pdb=" CG MET A 253 " pdb=" SD MET A 253 " ideal model delta sigma weight residual 112.70 124.58 -11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 11342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 4430 35.96 - 71.93: 416 71.93 - 107.89: 44 107.89 - 143.86: 6 143.86 - 179.82: 8 Dihedral angle restraints: 4904 sinusoidal: 3641 harmonic: 1263 Sorted by residual: dihedral pdb=" O4' U B 205 " pdb=" C1' U B 205 " pdb=" N1 U B 205 " pdb=" C2 U B 205 " ideal model delta sinusoidal sigma weight residual 232.00 56.67 175.33 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U B 274 " pdb=" C1' U B 274 " pdb=" N1 U B 274 " pdb=" C2 U B 274 " ideal model delta sinusoidal sigma weight residual 232.00 78.86 153.14 1 1.70e+01 3.46e-03 6.29e+01 dihedral pdb=" O4' U B 23 " pdb=" C1' U B 23 " pdb=" N1 U B 23 " pdb=" C2 U B 23 " ideal model delta sinusoidal sigma weight residual -160.00 -55.90 -104.10 1 1.50e+01 4.44e-03 5.31e+01 ... (remaining 4901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1094 0.046 - 0.091: 210 0.091 - 0.136: 69 0.136 - 0.182: 14 0.182 - 0.227: 5 Chirality restraints: 1392 Sorted by residual: chirality pdb=" C3' A B 161 " pdb=" C4' A B 161 " pdb=" O3' A B 161 " pdb=" C2' A B 161 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1' A B 148 " pdb=" O4' A B 148 " pdb=" C2' A B 148 " pdb=" N9 A B 148 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' A B 244 " pdb=" C4' A B 244 " pdb=" O3' A B 244 " pdb=" C2' A B 244 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 1389 not shown) Planarity restraints: 786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 9 " -0.042 2.00e-02 2.50e+03 2.19e-02 1.08e+01 pdb=" N1 C B 9 " 0.047 2.00e-02 2.50e+03 pdb=" C2 C B 9 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C B 9 " 0.007 2.00e-02 2.50e+03 pdb=" N3 C B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C B 9 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C B 9 " -0.017 2.00e-02 2.50e+03 pdb=" C5 C B 9 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C B 9 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 268 " -0.013 2.00e-02 2.50e+03 2.78e-02 7.72e+00 pdb=" C CYS A 268 " 0.048 2.00e-02 2.50e+03 pdb=" O CYS A 268 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 269 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 269 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C ASP A 269 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP A 269 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 270 " 0.015 2.00e-02 2.50e+03 ... (remaining 783 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 414 2.68 - 3.24: 7333 3.24 - 3.79: 13617 3.79 - 4.35: 15862 4.35 - 4.90: 22691 Nonbonded interactions: 59917 Sorted by model distance: nonbonded pdb=" N3 U B 173 " pdb=" O4 U B 186 " model vdw 2.128 3.120 nonbonded pdb=" O2' U B 133 " pdb=" OP1 U B 134 " model vdw 2.240 3.040 nonbonded pdb=" O2' G B 126 " pdb=" OP1 A B 127 " model vdw 2.292 3.040 nonbonded pdb=" O2' U B 262 " pdb=" OP1 C B 263 " model vdw 2.298 3.040 nonbonded pdb=" O VAL A 27 " pdb=" OG SER A 31 " model vdw 2.299 3.040 ... (remaining 59912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 7788 Z= 0.360 Angle : 0.801 11.885 11347 Z= 0.430 Chirality : 0.044 0.227 1392 Planarity : 0.005 0.032 786 Dihedral : 23.339 179.821 4090 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.84 % Favored : 96.69 % Rotamer: Outliers : 0.26 % Allowed : 5.25 % Favored : 94.49 % 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: 1.25 (0.41), residues: 423 helix: 1.63 (0.35), residues: 206 sheet: -0.09 (0.65), residues: 56 loop : 0.27 (0.53), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 260 TYR 0.014 0.002 TYR A 265 PHE 0.010 0.002 PHE A 47 TRP 0.007 0.002 TRP A 157 HIS 0.008 0.002 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 7788) covalent geometry : angle 0.80130 (11347) hydrogen bonds : bond 0.13932 ( 331) hydrogen bonds : angle 5.46683 ( 788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.177 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 11 average time/residue: 0.0686 time to fit residues: 1.3130 Evaluate side-chains 10 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.036306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.024044 restraints weight = 49603.912| |-----------------------------------------------------------------------------| r_work (start): 0.2360 rms_B_bonded: 2.92 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7788 Z= 0.146 Angle : 0.611 7.450 11347 Z= 0.317 Chirality : 0.036 0.206 1392 Planarity : 0.004 0.032 786 Dihedral : 24.669 179.634 3182 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.52 % Allowed : 6.56 % Favored : 92.91 % 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: 2.11 (0.42), residues: 423 helix: 2.52 (0.36), residues: 211 sheet: 0.29 (0.62), residues: 61 loop : 0.33 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 254 TYR 0.013 0.001 TYR A 279 PHE 0.010 0.001 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7788) covalent geometry : angle 0.61124 (11347) hydrogen bonds : bond 0.05167 ( 331) hydrogen bonds : angle 3.71453 ( 788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.179 Fit side-chains REVERT: A 319 MET cc_start: 0.9258 (mmm) cc_final: 0.9038 (mmm) outliers start: 2 outliers final: 1 residues processed: 13 average time/residue: 0.0589 time to fit residues: 1.3827 Evaluate side-chains 11 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.034739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.022406 restraints weight = 51217.480| |-----------------------------------------------------------------------------| r_work (start): 0.2293 rms_B_bonded: 3.15 r_work (final): 0.2293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 7788 Z= 0.341 Angle : 0.745 7.724 11347 Z= 0.384 Chirality : 0.042 0.234 1392 Planarity : 0.004 0.038 786 Dihedral : 24.761 175.850 3182 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.79 % Allowed : 7.09 % Favored : 92.13 % 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: 1.62 (0.41), residues: 423 helix: 2.16 (0.36), residues: 211 sheet: 0.52 (0.65), residues: 54 loop : -0.18 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 260 TYR 0.020 0.002 TYR A 279 PHE 0.014 0.002 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.007 0.002 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00695 ( 7788) covalent geometry : angle 0.74479 (11347) hydrogen bonds : bond 0.06518 ( 331) hydrogen bonds : angle 4.19713 ( 788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.199 Fit side-chains REVERT: A 319 MET cc_start: 0.9316 (mmm) cc_final: 0.8628 (mmm) REVERT: A 358 MET cc_start: 0.9345 (tmm) cc_final: 0.8912 (tmm) outliers start: 3 outliers final: 2 residues processed: 12 average time/residue: 0.0680 time to fit residues: 1.4672 Evaluate side-chains 12 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.0370 chunk 58 optimal weight: 10.0000 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.036745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.024429 restraints weight = 49012.046| |-----------------------------------------------------------------------------| r_work (start): 0.2380 rms_B_bonded: 3.00 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7788 Z= 0.118 Angle : 0.560 9.003 11347 Z= 0.292 Chirality : 0.035 0.199 1392 Planarity : 0.003 0.033 786 Dihedral : 24.585 178.297 3182 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.79 % Allowed : 7.61 % Favored : 91.60 % 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: 2.25 (0.43), residues: 423 helix: 2.74 (0.37), residues: 212 sheet: 0.50 (0.66), residues: 53 loop : 0.14 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 336 TYR 0.011 0.001 TYR A 279 PHE 0.010 0.001 PHE A 326 TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7788) covalent geometry : angle 0.55982 (11347) hydrogen bonds : bond 0.04704 ( 331) hydrogen bonds : angle 3.35775 ( 788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.212 Fit side-chains REVERT: A 358 MET cc_start: 0.9303 (tmm) cc_final: 0.8901 (tmm) outliers start: 3 outliers final: 2 residues processed: 12 average time/residue: 0.0616 time to fit residues: 1.4097 Evaluate side-chains 12 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 53 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.035201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.022816 restraints weight = 51066.733| |-----------------------------------------------------------------------------| r_work (start): 0.2319 rms_B_bonded: 3.15 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7788 Z= 0.295 Angle : 0.689 10.149 11347 Z= 0.352 Chirality : 0.039 0.221 1392 Planarity : 0.004 0.036 786 Dihedral : 24.643 177.881 3182 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.31 % Allowed : 7.61 % Favored : 91.08 % 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: 1.91 (0.42), residues: 423 helix: 2.53 (0.37), residues: 212 sheet: 0.31 (0.65), residues: 53 loop : -0.11 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.020 0.002 TYR A 279 PHE 0.011 0.001 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 7788) covalent geometry : angle 0.68949 (11347) hydrogen bonds : bond 0.05771 ( 331) hydrogen bonds : angle 3.83545 ( 788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.177 Fit side-chains REVERT: A 358 MET cc_start: 0.9369 (tmm) cc_final: 0.8912 (tmm) outliers start: 5 outliers final: 2 residues processed: 14 average time/residue: 0.0613 time to fit residues: 1.5016 Evaluate side-chains 12 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 45 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.036254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.023892 restraints weight = 49362.297| |-----------------------------------------------------------------------------| r_work (start): 0.2360 rms_B_bonded: 3.03 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7788 Z= 0.165 Angle : 0.587 9.849 11347 Z= 0.302 Chirality : 0.035 0.205 1392 Planarity : 0.003 0.036 786 Dihedral : 24.574 179.866 3182 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.79 % Allowed : 9.71 % Favored : 89.50 % 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: 2.23 (0.43), residues: 423 helix: 2.80 (0.37), residues: 212 sheet: 0.38 (0.65), residues: 53 loop : 0.05 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.014 0.001 TYR A 279 PHE 0.010 0.001 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7788) covalent geometry : angle 0.58749 (11347) hydrogen bonds : bond 0.04939 ( 331) hydrogen bonds : angle 3.47788 ( 788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.211 Fit side-chains REVERT: A 358 MET cc_start: 0.9340 (tmm) cc_final: 0.8911 (tmm) outliers start: 3 outliers final: 3 residues processed: 12 average time/residue: 0.0607 time to fit residues: 1.2968 Evaluate side-chains 13 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 314 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 0.3980 chunk 6 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.037095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.024635 restraints weight = 49073.173| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 3.06 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7788 Z= 0.119 Angle : 0.546 9.570 11347 Z= 0.281 Chirality : 0.033 0.195 1392 Planarity : 0.003 0.036 786 Dihedral : 24.531 178.363 3182 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.05 % Allowed : 9.45 % Favored : 89.50 % 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: 2.43 (0.43), residues: 423 helix: 2.97 (0.38), residues: 212 sheet: 0.43 (0.67), residues: 53 loop : 0.16 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 254 TYR 0.012 0.001 TYR A 279 PHE 0.008 0.001 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7788) covalent geometry : angle 0.54570 (11347) hydrogen bonds : bond 0.04413 ( 331) hydrogen bonds : angle 3.26962 ( 788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.119 Fit side-chains REVERT: A 358 MET cc_start: 0.9355 (tmm) cc_final: 0.8923 (tmm) outliers start: 4 outliers final: 3 residues processed: 13 average time/residue: 0.1177 time to fit residues: 2.1621 Evaluate side-chains 13 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 314 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.024251 restraints weight = 50328.776| |-----------------------------------------------------------------------------| r_work (start): 0.2384 rms_B_bonded: 3.09 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7788 Z= 0.174 Angle : 0.576 11.271 11347 Z= 0.295 Chirality : 0.034 0.202 1392 Planarity : 0.003 0.036 786 Dihedral : 24.530 179.048 3182 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.05 % Allowed : 9.71 % Favored : 89.24 % 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: 2.41 (0.43), residues: 423 helix: 2.97 (0.38), residues: 212 sheet: 0.39 (0.66), residues: 53 loop : 0.14 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.015 0.001 TYR A 279 PHE 0.008 0.001 PHE A 47 TRP 0.004 0.001 TRP A 157 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7788) covalent geometry : angle 0.57580 (11347) hydrogen bonds : bond 0.04648 ( 331) hydrogen bonds : angle 3.35222 ( 788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.183 Fit side-chains REVERT: A 358 MET cc_start: 0.9377 (tmm) cc_final: 0.8939 (tmm) outliers start: 4 outliers final: 3 residues processed: 13 average time/residue: 0.0620 time to fit residues: 1.4683 Evaluate side-chains 13 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.034978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.022668 restraints weight = 50505.428| |-----------------------------------------------------------------------------| r_work (start): 0.2314 rms_B_bonded: 3.15 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 7788 Z= 0.330 Angle : 0.732 11.705 11347 Z= 0.372 Chirality : 0.040 0.228 1392 Planarity : 0.004 0.038 786 Dihedral : 24.708 176.091 3182 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.79 % Allowed : 9.97 % Favored : 89.24 % 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: 1.81 (0.43), residues: 423 helix: 2.45 (0.37), residues: 212 sheet: 0.19 (0.67), residues: 53 loop : -0.13 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 260 TYR 0.020 0.002 TYR A 279 PHE 0.010 0.002 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 7788) covalent geometry : angle 0.73216 (11347) hydrogen bonds : bond 0.06243 ( 331) hydrogen bonds : angle 4.02837 ( 788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.177 Fit side-chains REVERT: A 358 MET cc_start: 0.9411 (tmm) cc_final: 0.8915 (tmm) outliers start: 3 outliers final: 3 residues processed: 12 average time/residue: 0.0648 time to fit residues: 1.4034 Evaluate side-chains 13 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 42 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.036052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.023662 restraints weight = 49893.852| |-----------------------------------------------------------------------------| r_work (start): 0.2359 rms_B_bonded: 3.04 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7788 Z= 0.179 Angle : 0.609 12.584 11347 Z= 0.310 Chirality : 0.035 0.204 1392 Planarity : 0.004 0.037 786 Dihedral : 24.624 179.532 3182 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.05 % Allowed : 9.45 % Favored : 89.50 % 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: 2.14 (0.43), residues: 423 helix: 2.76 (0.37), residues: 212 sheet: 0.27 (0.67), residues: 53 loop : -0.02 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 390 TYR 0.014 0.001 TYR A 279 PHE 0.010 0.001 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7788) covalent geometry : angle 0.60947 (11347) hydrogen bonds : bond 0.04998 ( 331) hydrogen bonds : angle 3.55807 ( 788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.217 Fit side-chains REVERT: A 358 MET cc_start: 0.9385 (tmm) cc_final: 0.8930 (tmm) outliers start: 4 outliers final: 3 residues processed: 13 average time/residue: 0.0627 time to fit residues: 1.5176 Evaluate side-chains 13 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.023540 restraints weight = 49818.726| |-----------------------------------------------------------------------------| r_work (start): 0.2354 rms_B_bonded: 3.03 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7788 Z= 0.207 Angle : 0.622 12.754 11347 Z= 0.316 Chirality : 0.036 0.207 1392 Planarity : 0.004 0.037 786 Dihedral : 24.612 179.523 3182 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.05 % Allowed : 9.45 % Favored : 89.50 % 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: 2.11 (0.43), residues: 423 helix: 2.74 (0.37), residues: 212 sheet: 0.27 (0.67), residues: 53 loop : -0.04 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.014 0.001 TYR A 279 PHE 0.011 0.001 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 7788) covalent geometry : angle 0.62189 (11347) hydrogen bonds : bond 0.05000 ( 331) hydrogen bonds : angle 3.58408 ( 788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1335.77 seconds wall clock time: 23 minutes 45.54 seconds (1425.54 seconds total)