Starting phenix.real_space_refine on Tue Aug 4 23:02:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jl3_61577/08_2026/9jl3_61577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jl3_61577/08_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_61577/08_2026/9jl3_61577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jl3_61577/08_2026/9jl3_61577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jl3_61577/08_2026/9jl3_61577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jl3_61577/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 1.79, per 1000 atoms: 0.25 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: 0.67 Conformation dependent library (CDL) restraints added in 317.0 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: 0.95 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: 1.30 Time building geometry restraints manager: 0.92 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: 10909 2.38 - 4.75: 408 4.75 - 7.13: 27 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=" O4' C B 9 " pdb=" C1' C B 9 " pdb=" N1 C B 9 " ideal model delta sigma weight residual 108.20 112.82 -4.62 8.00e-01 1.56e+00 3.34e+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=" O5' G B 227 " pdb=" C5' G B 227 " pdb=" C4' G B 227 " ideal model delta sigma weight residual 109.40 113.31 -3.91 8.00e-01 1.56e+00 2.39e+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: 925 0.046 - 0.091: 236 0.091 - 0.136: 203 0.136 - 0.182: 22 0.182 - 0.227: 6 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 1.07e+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: 1.320 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: 0.020 Set scattering table: 0.020 Process input model: 8.650 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.560 ------------------------------------------------------------------------------- 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= 0.558 Angle : 0.935 11.885 11347 Z= 0.747 Chirality : 0.060 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 0.00714 / 0.56 ( 7788) covalent geometry : angle 0.93525 / 0.75 (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 : 0.181 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 11 average time/residue: 0.0636 time to fit residues: 1.2595 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 : 0.138 ------------------------------------------------------------------------------- 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: 30.0000 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.036213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.023872 restraints weight = 49900.498| |-----------------------------------------------------------------------------| r_work (start): 0.2349 rms_B_bonded: 2.90 r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.0919 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= 0.138 Angle : 0.619 8.052 11347 Z= 0.351 Chirality : 0.043 0.384 1392 Planarity : 0.004 0.039 786 Dihedral : 24.784 178.341 3182 Min Nonbonded Distance : 2.297 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: 2.06 (0.35), residues: 210 sheet: 0.60 (0.65), residues: 53 loop : 0.15 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 204 TYR 0.016 0.001 TYR A 256 PHE 0.012 0.001 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.004 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.14 ( 7788) covalent geometry : angle 0.61930 / 0.35 (11347) hydrogen bonds : bond 0.06921 / 4.67 ( 331) hydrogen bonds : angle 4.07163 / 2.88 ( 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 : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0680 time to fit residues: 1.2518 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 : 0.195 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 40.0000 chunk 54 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 overall best weight: 4.0126 ------------------------------------------------------------------------------- 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 = 0.2856 r_free = 0.2856 target = 0.035697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.023451 restraints weight = 49612.889| |-----------------------------------------------------------------------------| r_work (start): 0.2352 rms_B_bonded: 2.93 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1115 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= 0.192 Angle : 0.623 7.966 11347 Z= 0.344 Chirality : 0.042 0.375 1392 Planarity : 0.004 0.038 786 Dihedral : 24.693 179.238 3182 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 2.01 (0.42), residues: 423 helix: 2.40 (0.36), residues: 212 sheet: 0.48 (0.66), residues: 53 loop : 0.23 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 260 TYR 0.015 0.001 TYR A 279 PHE 0.012 0.001 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.006 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 ( 7788) covalent geometry : angle 0.62313 / 0.34 (11347) hydrogen bonds : bond 0.06814 / 4.58 ( 331) hydrogen bonds : angle 3.91640 / 2.76 ( 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 12 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.188 Fit side-chains REVERT: A 319 MET cc_start: 0.9351 (mmm) cc_final: 0.8753 (mmm) REVERT: A 358 MET cc_start: 0.9342 (tmm) cc_final: 0.8787 (tmm) outliers start: 2 outliers final: 2 residues processed: 11 average time/residue: 0.0646 time to fit residues: 1.2920 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 : 0.212 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 30.0000 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 chunk 58 optimal weight: 20.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- 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 = 0.2859 r_free = 0.2859 target = 0.036002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.023622 restraints weight = 50208.551| |-----------------------------------------------------------------------------| r_work (start): 0.2356 rms_B_bonded: 3.06 r_work (final): 0.2356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1448 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= 0.159 Angle : 0.561 8.554 11347 Z= 0.315 Chirality : 0.041 0.374 1392 Planarity : 0.004 0.036 786 Dihedral : 24.615 179.941 3182 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 2.10 (0.42), residues: 423 helix: 2.55 (0.36), residues: 212 sheet: 0.43 (0.66), residues: 53 loop : 0.18 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 254 TYR 0.013 0.001 TYR A 279 PHE 0.013 0.001 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 ( 7788) covalent geometry : angle 0.56126 / 0.32 (11347) hydrogen bonds : bond 0.06188 / 4.21 ( 331) hydrogen bonds : angle 3.67303 / 2.58 ( 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: 3 poor density : 12 time to evaluate : 0.232 Fit side-chains REVERT: A 358 MET cc_start: 0.9375 (tmm) cc_final: 0.8843 (tmm) outliers start: 3 outliers final: 2 residues processed: 14 average time/residue: 0.0559 time to fit residues: 1.4389 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 : 0.184 ------------------------------------------------------------------------------- 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: 30.0000 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 40.0000 chunk 18 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 0.0270 chunk 46 optimal weight: 50.0000 overall best weight: 4.2046 ------------------------------------------------------------------------------- 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 = 0.2859 r_free = 0.2859 target = 0.035883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.023488 restraints weight = 50436.826| |-----------------------------------------------------------------------------| r_work (start): 0.2352 rms_B_bonded: 3.02 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1516 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= 0.192 Angle : 0.586 8.404 11347 Z= 0.323 Chirality : 0.041 0.377 1392 Planarity : 0.004 0.037 786 Dihedral : 24.582 179.789 3182 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.05 % Allowed : 7.61 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.42), residues: 423 helix: 2.59 (0.37), residues: 212 sheet: 0.31 (0.64), residues: 53 loop : 0.07 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 ( 7788) covalent geometry : angle 0.58620 / 0.32 (11347) hydrogen bonds : bond 0.06299 / 4.28 ( 331) hydrogen bonds : angle 3.70957 / 2.60 ( 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 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: 0.9393 (tmm) cc_final: 0.8857 (tmm) outliers start: 4 outliers final: 3 residues processed: 13 average time/residue: 0.0567 time to fit residues: 1.3509 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 45 optimal weight: 40.0000 chunk 19 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 43 optimal weight: 40.0000 chunk 11 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.2875 r_free = 0.2875 target = 0.036383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.024038 restraints weight = 49416.410| |-----------------------------------------------------------------------------| r_work (start): 0.2376 rms_B_bonded: 3.05 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7788 Z= 0.132 Angle : 0.546 8.652 11347 Z= 0.302 Chirality : 0.039 0.368 1392 Planarity : 0.003 0.035 786 Dihedral : 24.529 179.376 3182 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.31 % Allowed : 7.09 % 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: 2.21 (0.43), residues: 423 helix: 2.74 (0.37), residues: 212 sheet: 0.39 (0.65), residues: 53 loop : 0.11 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 204 TYR 0.013 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 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 ( 7788) covalent geometry : angle 0.54581 / 0.30 (11347) hydrogen bonds : bond 0.05881 / 4.00 ( 331) hydrogen bonds : angle 3.51372 / 2.45 ( 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 15 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.190 Fit side-chains REVERT: A 358 MET cc_start: 0.9391 (tmm) cc_final: 0.8881 (tmm) outliers start: 5 outliers final: 2 residues processed: 15 average time/residue: 0.0612 time to fit residues: 1.6152 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 : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 235 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.2866 r_free = 0.2866 target = 0.036052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.023759 restraints weight = 49742.388| |-----------------------------------------------------------------------------| r_work (start): 0.2361 rms_B_bonded: 3.00 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7788 Z= 0.199 Angle : 0.601 10.679 11347 Z= 0.322 Chirality : 0.041 0.375 1392 Planarity : 0.004 0.036 786 Dihedral : 24.524 179.756 3182 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.05 % Allowed : 8.14 % Favored : 90.81 % 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: 2.67 (0.37), residues: 212 sheet: 0.33 (0.66), residues: 53 loop : 0.05 (0.51), 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 0.004 0.001 TRP A 157 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 ( 7788) covalent geometry : angle 0.60137 / 0.32 (11347) hydrogen bonds : bond 0.06028 / 4.08 ( 331) hydrogen bonds : angle 3.65313 / 2.56 ( 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 : 0.189 Fit side-chains REVERT: A 358 MET cc_start: 0.9403 (tmm) cc_final: 0.8882 (tmm) outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.0602 time to fit residues: 1.4233 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 : 0.266 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.2894 r_free = 0.2894 target = 0.036873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.024505 restraints weight = 49562.939| |-----------------------------------------------------------------------------| r_work (start): 0.2395 rms_B_bonded: 3.04 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2032 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= 0.109 Angle : 0.544 11.014 11347 Z= 0.294 Chirality : 0.038 0.363 1392 Planarity : 0.003 0.035 786 Dihedral : 24.484 178.746 3182 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.05 % Allowed : 8.40 % Favored : 90.55 % 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: 2.35 (0.43), residues: 423 helix: 2.84 (0.37), residues: 212 sheet: 0.38 (0.66), residues: 53 loop : 0.23 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 254 TYR 0.012 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 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.11 ( 7788) covalent geometry : angle 0.54447 / 0.29 (11347) hydrogen bonds : bond 0.05607 / 3.80 ( 331) hydrogen bonds : angle 3.40852 / 2.37 ( 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 : 0.190 Fit side-chains REVERT: A 358 MET cc_start: 0.9401 (tmm) cc_final: 0.8896 (tmm) outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.0609 time to fit residues: 1.4400 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 : 0.178 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 0.0670 chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 56 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 overall best weight: 2.9924 ------------------------------------------------------------------------------- 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 = 0.2886 r_free = 0.2886 target = 0.036640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.024282 restraints weight = 49427.234| |-----------------------------------------------------------------------------| r_work (start): 0.2382 rms_B_bonded: 3.00 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2028 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= 0.143 Angle : 0.565 11.926 11347 Z= 0.301 Chirality : 0.039 0.368 1392 Planarity : 0.003 0.035 786 Dihedral : 24.466 179.084 3182 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.79 % Allowed : 8.92 % 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: 2.29 (0.43), residues: 423 helix: 2.78 (0.37), residues: 213 sheet: 0.29 (0.66), residues: 53 loop : 0.23 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.013 0.001 TYR A 279 PHE 0.009 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/Z covalent geometry : bond 0.00275 / 0.14 ( 7788) covalent geometry : angle 0.56507 / 0.30 (11347) hydrogen bonds : bond 0.05703 / 3.86 ( 331) hydrogen bonds : angle 3.45039 / 2.41 ( 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 : 0.195 Fit side-chains REVERT: A 358 MET cc_start: 0.9399 (tmm) cc_final: 0.8892 (tmm) outliers start: 3 outliers final: 3 residues processed: 12 average time/residue: 0.0570 time to fit residues: 1.2546 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 : 0.187 ------------------------------------------------------------------------------- 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 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 42 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 overall best weight: 4.0586 ------------------------------------------------------------------------------- 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 = 0.2878 r_free = 0.2878 target = 0.036421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.024048 restraints weight = 50156.394| |-----------------------------------------------------------------------------| r_work (start): 0.2372 rms_B_bonded: 3.01 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2016 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= 0.189 Angle : 0.596 12.072 11347 Z= 0.314 Chirality : 0.040 0.371 1392 Planarity : 0.004 0.036 786 Dihedral : 24.465 179.345 3182 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 2.22 (0.43), residues: 423 helix: 2.75 (0.37), residues: 213 sheet: 0.22 (0.66), residues: 53 loop : 0.16 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 ( 7788) covalent geometry : angle 0.59565 / 0.31 (11347) hydrogen bonds : bond 0.05747 / 3.89 ( 331) hydrogen bonds : angle 3.55975 / 2.49 ( 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 : 0.116 Fit side-chains REVERT: A 358 MET cc_start: 0.9414 (tmm) cc_final: 0.8905 (tmm) outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.0493 time to fit residues: 1.1579 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 : 0.202 ------------------------------------------------------------------------------- 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: 40.0000 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 30.0000 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.0270 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.4442 ------------------------------------------------------------------------------- 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 = 0.2906 r_free = 0.2906 target = 0.037218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.024768 restraints weight = 48768.819| |-----------------------------------------------------------------------------| r_work (start): 0.2409 rms_B_bonded: 3.02 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2258 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= 0.104 Angle : 0.544 11.990 11347 Z= 0.289 Chirality : 0.038 0.357 1392 Planarity : 0.003 0.035 786 Dihedral : 24.436 178.555 3182 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 2.45 (0.43), residues: 423 helix: 2.88 (0.38), residues: 213 sheet: 0.41 (0.66), residues: 53 loop : 0.33 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 254 TYR 0.011 0.001 TYR A 279 PHE 0.009 0.001 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.10 ( 7788) covalent geometry : angle 0.54362 / 0.29 (11347) hydrogen bonds : bond 0.05408 / 3.65 ( 331) hydrogen bonds : angle 3.32396 / 2.31 ( 788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1302.34 seconds wall clock time: 23 minutes 8.61 seconds (1388.61 seconds total)