Starting phenix.real_space_refine on Thu Jul 2 06:49:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jl3_61577/07_2026/9jl3_61577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jl3_61577/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jl3_61577/07_2026/9jl3_61577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jl3_61577/07_2026/9jl3_61577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jl3_61577/07_2026/9jl3_61577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jl3_61577/07_2026/9jl3_61577.map" } 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-dev-6108/lib/python3.11/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: 1.13, per 1000 atoms: 0.16 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: 0.53 Conformation dependent library (CDL) restraints added in 161.0 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: 0.72 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: 1.12 Time building geometry restraints manager: 0.61 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=" N9 G B 160 " pdb=" C4 G B 160 " ideal model delta sigma weight residual 1.375 1.351 0.024 8.00e-03 1.56e+04 8.84e+00 bond pdb=" N9 A B 200 " pdb=" C4 A B 200 " ideal model delta sigma weight residual 1.374 1.358 0.016 6.00e-03 2.78e+04 6.85e+00 ... (remaining 7783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 11124 2.38 - 4.75: 195 4.75 - 7.13: 25 7.13 - 9.51: 1 9.51 - 11.88: 2 Bond angle restraints: 11347 Sorted by residual: angle pdb=" C1' C B 124 " pdb=" N1 C B 124 " pdb=" C2 C B 124 " ideal model delta sigma weight residual 118.80 125.79 -6.99 1.10e+00 8.26e-01 4.03e+01 angle pdb=" C1' C B 124 " pdb=" N1 C B 124 " pdb=" C6 C B 124 " ideal model delta sigma weight residual 120.80 114.56 6.24 1.20e+00 6.94e-01 2.70e+01 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 ... (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: 1090 0.046 - 0.091: 212 0.091 - 0.136: 71 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: 0.950 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.700 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 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= 0.536 Angle : 0.803 11.885 11347 Z= 0.636 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/Z covalent geometry : bond 0.00700 / 0.54 ( 7788) covalent geometry : angle 0.80265 / 0.64 (11347) hydrogen bonds : bond 0.13932 / 8.80 ( 331) hydrogen bonds : angle 5.46683 / 3.88 ( 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 : 0.110 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 11 average time/residue: 0.0458 time to fit residues: 0.9475 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 : 0.126 ------------------------------------------------------------------------------- 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: 20.0000 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 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: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.2864 r_free = 0.2864 target = 0.035966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.023686 restraints weight = 49567.448| |-----------------------------------------------------------------------------| r_work (start): 0.2343 rms_B_bonded: 2.92 r_work (final): 0.2343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7788 Z= 0.152 Angle : 0.583 6.975 11347 Z= 0.348 Chirality : 0.040 0.230 1392 Planarity : 0.004 0.039 786 Dihedral : 24.845 178.083 3182 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: 1.70 (0.41), residues: 423 helix: 2.07 (0.35), residues: 210 sheet: 0.59 (0.65), residues: 53 loop : 0.12 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 204 TYR 0.016 0.002 TYR A 256 PHE 0.013 0.001 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 ( 7788) covalent geometry : angle 0.58313 / 0.35 (11347) hydrogen bonds : bond 0.06715 / 4.54 ( 331) hydrogen bonds : angle 4.08449 / 2.89 ( 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 10 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.109 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0534 time to fit residues: 0.9419 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 : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 chunk 22 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 overall best weight: 3.8184 ------------------------------------------------------------------------------- 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 = 0.2854 r_free = 0.2854 target = 0.035649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.023336 restraints weight = 50066.453| |-----------------------------------------------------------------------------| r_work (start): 0.2329 rms_B_bonded: 2.96 r_work (final): 0.2329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7788 Z= 0.188 Angle : 0.568 7.281 11347 Z= 0.334 Chirality : 0.038 0.212 1392 Planarity : 0.004 0.039 786 Dihedral : 24.789 179.152 3182 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.52 % Allowed : 7.09 % Favored : 92.39 % 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: 2.02 (0.42), residues: 423 helix: 2.42 (0.36), residues: 212 sheet: 0.47 (0.66), residues: 53 loop : 0.22 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.015 0.001 TYR A 279 PHE 0.011 0.001 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 ( 7788) covalent geometry : angle 0.56817 / 0.33 (11347) hydrogen bonds : bond 0.06484 / 4.35 ( 331) hydrogen bonds : angle 3.87070 / 2.73 ( 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: 2 poor density : 11 time to evaluate : 0.197 Fit side-chains REVERT: A 319 MET cc_start: 0.9340 (mmm) cc_final: 0.8703 (mmm) REVERT: A 358 MET cc_start: 0.9312 (tmm) cc_final: 0.8773 (tmm) outliers start: 2 outliers final: 2 residues processed: 12 average time/residue: 0.0476 time to fit residues: 1.1272 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 : 0.115 ------------------------------------------------------------------------------- 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: 6.9990 chunk 47 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.034960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2339 r_free = 0.2339 target = 0.022570 restraints weight = 51324.952| |-----------------------------------------------------------------------------| r_work (start): 0.2305 rms_B_bonded: 3.23 r_work (final): 0.2305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7788 Z= 0.261 Angle : 0.616 7.605 11347 Z= 0.357 Chirality : 0.040 0.220 1392 Planarity : 0.004 0.041 786 Dihedral : 24.746 178.147 3182 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: 1.66 (0.41), residues: 423 helix: 2.25 (0.36), residues: 212 sheet: 0.19 (0.65), 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 0.017 0.002 TYR A 279 PHE 0.014 0.002 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.005 0.002 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.26 ( 7788) covalent geometry : angle 0.61574 / 0.36 (11347) hydrogen bonds : bond 0.06665 / 4.52 ( 331) hydrogen bonds : angle 3.99414 / 2.82 ( 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 15 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.112 Fit side-chains REVERT: A 358 MET cc_start: 0.9390 (tmm) cc_final: 0.8848 (tmm) outliers start: 5 outliers final: 2 residues processed: 14 average time/residue: 0.0455 time to fit residues: 1.1153 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 : 0.216 ------------------------------------------------------------------------------- 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: 20.0000 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 40.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2849 r_free = 0.2849 target = 0.035607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.023328 restraints weight = 50064.058| |-----------------------------------------------------------------------------| r_work (start): 0.2334 rms_B_bonded: 3.06 r_work (final): 0.2334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7788 Z= 0.155 Angle : 0.541 9.621 11347 Z= 0.317 Chirality : 0.037 0.209 1392 Planarity : 0.004 0.037 786 Dihedral : 24.699 179.360 3182 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.57 % Allowed : 7.35 % 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: 1.98 (0.42), residues: 423 helix: 2.55 (0.37), residues: 212 sheet: 0.23 (0.65), residues: 53 loop : 0.02 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 254 TYR 0.015 0.001 TYR A 279 PHE 0.011 0.001 PHE A 326 TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 ( 7788) covalent geometry : angle 0.54140 / 0.32 (11347) hydrogen bonds : bond 0.06133 / 4.16 ( 331) hydrogen bonds : angle 3.67965 / 2.59 ( 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 17 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.187 Fit side-chains REVERT: A 358 MET cc_start: 0.9396 (tmm) cc_final: 0.8834 (tmm) outliers start: 6 outliers final: 4 residues processed: 16 average time/residue: 0.0522 time to fit residues: 1.5329 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 : 0.181 ------------------------------------------------------------------------------- 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 235 SER Chi-restraints excluded: chain A residue 314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 45 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 43 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2836 r_free = 0.2836 target = 0.035243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.022953 restraints weight = 50118.403| |-----------------------------------------------------------------------------| r_work (start): 0.2321 rms_B_bonded: 3.06 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7788 Z= 0.241 Angle : 0.593 10.635 11347 Z= 0.340 Chirality : 0.039 0.219 1392 Planarity : 0.004 0.038 786 Dihedral : 24.676 179.006 3182 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.05 % Allowed : 8.66 % Favored : 90.29 % 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 (0.42), residues: 423 helix: 2.45 (0.36), residues: 212 sheet: 0.14 (0.65), residues: 53 loop : -0.12 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.017 0.002 TYR A 279 PHE 0.010 0.001 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.24 ( 7788) covalent geometry : angle 0.59257 / 0.34 (11347) hydrogen bonds : bond 0.06324 / 4.28 ( 331) hydrogen bonds : angle 3.83067 / 2.70 ( 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 14 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.187 Fit side-chains REVERT: A 358 MET cc_start: 0.9420 (tmm) cc_final: 0.8858 (tmm) outliers start: 4 outliers final: 3 residues processed: 13 average time/residue: 0.0509 time to fit residues: 1.2361 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 : 0.115 ------------------------------------------------------------------------------- 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: 10.0000 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2872 r_free = 0.2872 target = 0.036232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.023895 restraints weight = 48753.108| |-----------------------------------------------------------------------------| r_work (start): 0.2363 rms_B_bonded: 3.02 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7788 Z= 0.119 Angle : 0.536 11.819 11347 Z= 0.306 Chirality : 0.036 0.203 1392 Planarity : 0.004 0.036 786 Dihedral : 24.616 179.449 3182 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: 2.17 (0.43), residues: 423 helix: 2.74 (0.37), residues: 212 sheet: 0.26 (0.65), residues: 53 loop : 0.08 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 254 TYR 0.013 0.001 TYR A 279 PHE 0.011 0.001 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 ( 7788) covalent geometry : angle 0.53596 / 0.31 (11347) hydrogen bonds : bond 0.05713 / 3.87 ( 331) hydrogen bonds : angle 3.51897 / 2.47 ( 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: 3 poor density : 11 time to evaluate : 0.216 Fit side-chains REVERT: A 358 MET cc_start: 0.9402 (tmm) cc_final: 0.8895 (tmm) outliers start: 3 outliers final: 3 residues processed: 14 average time/residue: 0.0634 time to fit residues: 1.5700 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 235 SER 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: 9.9990 chunk 27 optimal weight: 0.0270 chunk 24 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2858 r_free = 0.2858 target = 0.035783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.023442 restraints weight = 50616.111| |-----------------------------------------------------------------------------| r_work (start): 0.2351 rms_B_bonded: 3.03 r_work (final): 0.2351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7788 Z= 0.188 Angle : 0.561 11.528 11347 Z= 0.319 Chirality : 0.037 0.212 1392 Planarity : 0.004 0.037 786 Dihedral : 24.600 179.984 3182 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.30 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: 2.12 (0.43), residues: 423 helix: 2.69 (0.37), residues: 212 sheet: 0.28 (0.66), residues: 53 loop : 0.06 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 254 TYR 0.015 0.001 TYR A 279 PHE 0.010 0.001 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 ( 7788) covalent geometry : angle 0.56133 / 0.32 (11347) hydrogen bonds : bond 0.05916 / 3.99 ( 331) hydrogen bonds : angle 3.62570 / 2.55 ( 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 : 0.182 Fit side-chains REVERT: A 358 MET cc_start: 0.9416 (tmm) cc_final: 0.8901 (tmm) outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.0537 time to fit residues: 1.2826 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 : 0.186 ------------------------------------------------------------------------------- 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 235 SER 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: 3.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2859 r_free = 0.2859 target = 0.035757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.023408 restraints weight = 49534.962| |-----------------------------------------------------------------------------| r_work (start): 0.2352 rms_B_bonded: 3.00 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1828 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= 0.187 Angle : 0.564 12.350 11347 Z= 0.320 Chirality : 0.037 0.210 1392 Planarity : 0.004 0.037 786 Dihedral : 24.597 179.978 3182 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.05 % Allowed : 9.97 % Favored : 88.98 % 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: 2.10 (0.43), residues: 423 helix: 2.68 (0.37), residues: 212 sheet: 0.30 (0.67), residues: 53 loop : 0.02 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.015 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 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 ( 7788) covalent geometry : angle 0.56396 / 0.32 (11347) hydrogen bonds : bond 0.05895 / 3.99 ( 331) hydrogen bonds : angle 3.64660 / 2.56 ( 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 14 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.116 Fit side-chains REVERT: A 358 MET cc_start: 0.9427 (tmm) cc_final: 0.8886 (tmm) outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.0544 time to fit residues: 1.2575 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 : 0.187 ------------------------------------------------------------------------------- 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 235 SER 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: 20.0000 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2856 r_free = 0.2856 target = 0.035721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.023382 restraints weight = 50065.752| |-----------------------------------------------------------------------------| r_work (start): 0.2350 rms_B_bonded: 3.03 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1835 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= 0.201 Angle : 0.572 12.810 11347 Z= 0.323 Chirality : 0.037 0.212 1392 Planarity : 0.004 0.037 786 Dihedral : 24.594 179.913 3182 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.05 % Allowed : 9.97 % Favored : 88.98 % 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: 2.09 (0.43), residues: 423 helix: 2.68 (0.37), residues: 212 sheet: 0.28 (0.67), residues: 53 loop : 0.02 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.016 0.001 TYR A 279 PHE 0.010 0.001 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 ( 7788) covalent geometry : angle 0.57209 / 0.32 (11347) hydrogen bonds : bond 0.05912 / 4.00 ( 331) hydrogen bonds : angle 3.66085 / 2.58 ( 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 : 0.188 Fit side-chains REVERT: A 358 MET cc_start: 0.9426 (tmm) cc_final: 0.8885 (tmm) outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.0590 time to fit residues: 1.3416 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 ------------------------------------------------------------------------------- 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 235 SER 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: 30.0000 chunk 11 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.023764 restraints weight = 49197.348| |-----------------------------------------------------------------------------| r_work (start): 0.2365 rms_B_bonded: 3.02 r_work (final): 0.2365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7788 Z= 0.140 Angle : 0.538 12.526 11347 Z= 0.304 Chirality : 0.036 0.204 1392 Planarity : 0.003 0.036 786 Dihedral : 24.564 179.509 3182 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.79 % Allowed : 10.76 % Favored : 88.45 % 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: 2.28 (0.43), residues: 423 helix: 2.82 (0.37), residues: 212 sheet: 0.32 (0.67), residues: 53 loop : 0.15 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 254 TYR 0.014 0.001 TYR A 279 PHE 0.010 0.001 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 ( 7788) covalent geometry : angle 0.53824 / 0.30 (11347) hydrogen bonds : bond 0.05632 / 3.80 ( 331) hydrogen bonds : angle 3.49661 / 2.45 ( 788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1121.71 seconds wall clock time: 20 minutes 9.60 seconds (1209.60 seconds total)