Starting phenix.real_space_refine on Wed Aug 5 13:16:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ziz_74289/08_2026/9ziz_74289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ziz_74289/08_2026/9ziz_74289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ziz_74289/08_2026/9ziz_74289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ziz_74289/08_2026/9ziz_74289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ziz_74289/08_2026/9ziz_74289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ziz_74289/08_2026/9ziz_74289.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 417 5.49 5 Mg 40 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s 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: 9949 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 30, 'rna2p_pyr': 22, 'rna3p_pur': 213, 'rna3p_pyr': 152} Link IDs: {'rna2p': 52, 'rna3p': 364} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 947 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Unusual residues: {' MG': 40} Classifications: {'undetermined': 40} Link IDs: {None: 39} Time building chain proxies: 2.16, per 1000 atoms: 0.22 Number of scatterers: 9949 At special positions: 0 Unit cell: (92.232, 170.556, 147.132, 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 3 16.00 P 417 15.00 Mg 40 11.99 O 3051 8.00 N 1834 7.00 C 4604 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: 0.70 Conformation dependent library (CDL) restraints added in 75.0 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 1 sheets defined 48.3% alpha, 13.8% beta 133 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.567A pdb=" N PHE B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.650A pdb=" N GLY B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 34 removed outlier: 3.750A pdb=" N ARG B 42 " --> pdb=" O LYS B 79 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 580 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.01 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: 1173 1.33 - 1.45: 5220 1.45 - 1.57: 3769 1.57 - 1.68: 833 1.68 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" C2 C A 260 " pdb=" O2 C A 260 " ideal model delta sigma weight residual 1.240 1.216 0.024 9.00e-03 1.23e+04 6.87e+00 bond pdb=" N3 G A 273 " pdb=" C4 G A 273 " ideal model delta sigma weight residual 1.350 1.334 0.016 7.00e-03 2.04e+04 5.22e+00 bond pdb=" C2 G A 273 " pdb=" N3 G A 273 " ideal model delta sigma weight residual 1.323 1.306 0.017 8.00e-03 1.56e+04 4.74e+00 bond pdb=" N9 G A 273 " pdb=" C4 G A 273 " ideal model delta sigma weight residual 1.375 1.358 0.017 8.00e-03 1.56e+04 4.73e+00 bond pdb=" N9 G A 265 " pdb=" C4 G A 265 " ideal model delta sigma weight residual 1.375 1.392 -0.017 8.00e-03 1.56e+04 4.56e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.57: 16927 5.57 - 11.15: 12 11.15 - 16.72: 1 16.72 - 22.30: 0 22.30 - 27.87: 4 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O3' U A 384 " pdb=" P A A 385 " pdb=" OP2 A A 385 " ideal model delta sigma weight residual 108.00 80.13 27.87 3.00e+00 1.11e-01 8.63e+01 angle pdb=" O3' G A 345 " pdb=" P C A 346 " pdb=" OP1 C A 346 " ideal model delta sigma weight residual 108.00 81.33 26.67 3.00e+00 1.11e-01 7.91e+01 angle pdb=" O3' G A 345 " pdb=" P C A 346 " pdb=" OP2 C A 346 " ideal model delta sigma weight residual 108.00 83.61 24.39 3.00e+00 1.11e-01 6.61e+01 angle pdb=" O3' U A 384 " pdb=" P A A 385 " pdb=" OP1 A A 385 " ideal model delta sigma weight residual 108.00 85.20 22.80 3.00e+00 1.11e-01 5.78e+01 angle pdb=" C1' C A 347 " pdb=" N1 C A 347 " pdb=" C2 C A 347 " ideal model delta sigma weight residual 118.80 126.80 -8.00 1.10e+00 8.26e-01 5.29e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 5960 35.46 - 70.93: 1011 70.93 - 106.39: 138 106.39 - 141.85: 5 141.85 - 177.32: 2 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' C A 347 " pdb=" C1' C A 347 " pdb=" N1 C A 347 " pdb=" C2 C A 347 " ideal model delta sinusoidal sigma weight residual 200.00 82.68 117.32 1 1.50e+01 4.44e-03 6.23e+01 dihedral pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sinusoidal sigma weight residual -160.00 -43.30 -116.70 1 1.50e+01 4.44e-03 6.18e+01 dihedral pdb=" O4' U A 35 " pdb=" C1' U A 35 " pdb=" N1 U A 35 " pdb=" C2 U A 35 " ideal model delta sinusoidal sigma weight residual -160.00 -83.41 -76.59 1 1.50e+01 4.44e-03 3.28e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.401: 2219 0.401 - 0.802: 0 0.802 - 1.203: 0 1.203 - 1.605: 0 1.605 - 2.006: 2 Chirality restraints: 2221 Sorted by residual: chirality pdb=" P A A 385 " pdb=" OP1 A A 385 " pdb=" OP2 A A 385 " pdb=" O5' A A 385 " both_signs ideal model delta sigma weight residual True 2.41 0.40 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" P C A 346 " pdb=" OP1 C A 346 " pdb=" OP2 C A 346 " pdb=" O5' C A 346 " both_signs ideal model delta sigma weight residual True 2.41 0.45 1.96 2.00e-01 2.50e+01 9.56e+01 chirality pdb=" C1' C A 359 " pdb=" O4' C A 359 " pdb=" C2' C A 359 " pdb=" N1 C A 359 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 260 " -0.004 2.00e-02 2.50e+03 3.17e-02 2.26e+01 pdb=" N1 C A 260 " 0.008 2.00e-02 2.50e+03 pdb=" C2 C A 260 " -0.077 2.00e-02 2.50e+03 pdb=" O2 C A 260 " 0.047 2.00e-02 2.50e+03 pdb=" N3 C A 260 " 0.010 2.00e-02 2.50e+03 pdb=" C4 C A 260 " -0.017 2.00e-02 2.50e+03 pdb=" N4 C A 260 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C A 260 " 0.010 2.00e-02 2.50e+03 pdb=" C6 C A 260 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 273 " -0.015 2.00e-02 2.50e+03 1.93e-02 1.12e+01 pdb=" N9 G A 273 " 0.008 2.00e-02 2.50e+03 pdb=" C8 G A 273 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 273 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 273 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 273 " 0.015 2.00e-02 2.50e+03 pdb=" O6 G A 273 " -0.017 2.00e-02 2.50e+03 pdb=" N1 G A 273 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G A 273 " 0.052 2.00e-02 2.50e+03 pdb=" N2 G A 273 " -0.031 2.00e-02 2.50e+03 pdb=" N3 G A 273 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G A 273 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.036 2.00e-02 2.50e+03 1.56e-02 7.27e+00 pdb=" N9 G A 298 " -0.037 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.004 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 43 2.53 - 3.12: 6973 3.12 - 3.71: 21363 3.71 - 4.31: 27902 4.31 - 4.90: 35632 Nonbonded interactions: 91913 Sorted by model distance: nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 512 " model vdw 1.937 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 512 " model vdw 1.954 2.170 nonbonded pdb=" OP2 G A 47 " pdb="MG MG A 517 " model vdw 1.973 2.170 nonbonded pdb=" OP1 A A 50 " pdb="MG MG A 505 " model vdw 1.990 2.170 nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 509 " model vdw 1.992 2.170 ... (remaining 91908 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: 9.950 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: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.660 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 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 : 0.003 0.041 11000 Z= 0.270 Angle : 0.945 27.871 16944 Z= 0.753 Chirality : 0.086 2.006 2221 Planarity : 0.004 0.032 581 Dihedral : 25.680 177.318 6900 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 2.02 % Allowed : 34.34 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.87), residues: 114 helix: 1.38 (0.80), residues: 47 sheet: -2.59 (0.94), residues: 26 loop : -2.25 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 106 TYR 0.009 0.001 TYR B 31 PHE 0.006 0.001 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.27 (11000) covalent geometry : angle 0.94505 / 0.75 (16944) hydrogen bonds : bond 0.10597 / 11.58 ( 384) hydrogen bonds : angle 5.02587 / 7.12 ( 709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.235 Fit side-chains REVERT: B 15 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 74 GLU cc_start: 0.8897 (mp0) cc_final: 0.8542 (mp0) outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0926 time to fit residues: 2.7084 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 40.0000 chunk 30 optimal weight: 10.0000 overall best weight: 7.5590 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.074184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.043703 restraints weight = 63598.761| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.93 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 11000 Z= 0.522 Angle : 1.076 29.875 16944 Z= 0.523 Chirality : 0.087 1.867 2221 Planarity : 0.007 0.040 581 Dihedral : 25.864 179.894 6649 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 28.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 7.07 % Allowed : 24.24 % Favored : 68.69 % 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: -1.95 (0.82), residues: 114 helix: 0.42 (0.75), residues: 47 sheet: -2.60 (0.93), residues: 26 loop : -2.30 (1.09), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 42 TYR 0.023 0.004 TYR B 5 PHE 0.013 0.003 PHE B 13 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00799 / 0.52 (11000) covalent geometry : angle 1.07574 / 0.52 (16944) hydrogen bonds : bond 0.13492 / 13.88 ( 384) hydrogen bonds : angle 3.51665 / 4.51 ( 709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.148 Fit side-chains REVERT: B 15 GLU cc_start: 0.8693 (tm-30) cc_final: 0.7747 (tm-30) outliers start: 7 outliers final: 5 residues processed: 20 average time/residue: 0.0901 time to fit residues: 2.7504 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 50.0000 chunk 30 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.073698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.043753 restraints weight = 63308.864| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.73 r_work: 0.2700 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 11000 Z= 0.394 Angle : 0.933 29.287 16944 Z= 0.460 Chirality : 0.080 1.859 2221 Planarity : 0.006 0.033 581 Dihedral : 26.102 177.154 6649 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 11.11 % Allowed : 24.24 % Favored : 64.65 % 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 (0.82), residues: 114 helix: 0.43 (0.75), residues: 47 sheet: -3.15 (0.86), residues: 26 loop : -2.26 (1.11), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 42 TYR 0.025 0.003 TYR B 5 PHE 0.018 0.004 PHE B 17 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.39 (11000) covalent geometry : angle 0.93343 / 0.46 (16944) hydrogen bonds : bond 0.11967 / 12.39 ( 384) hydrogen bonds : angle 3.43407 / 4.31 ( 709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 15 time to evaluate : 0.085 Fit side-chains REVERT: B 15 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8188 (tm-30) outliers start: 11 outliers final: 6 residues processed: 24 average time/residue: 0.1068 time to fit residues: 3.6128 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 9.9990 chunk 36 optimal weight: 40.0000 chunk 12 optimal weight: 30.0000 chunk 41 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 overall best weight: 5.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.073165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.043359 restraints weight = 64521.954| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.07 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11000 Z= 0.409 Angle : 0.964 29.086 16944 Z= 0.474 Chirality : 0.081 1.867 2221 Planarity : 0.006 0.033 581 Dihedral : 26.149 176.101 6649 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 28.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 7.07 % Allowed : 30.30 % Favored : 62.63 % 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: -2.06 (0.83), residues: 114 helix: 0.27 (0.75), residues: 46 sheet: -3.11 (0.87), residues: 26 loop : -1.88 (1.15), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 42 TYR 0.020 0.003 TYR B 5 PHE 0.010 0.003 PHE B 28 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.41 (11000) covalent geometry : angle 0.96388 / 0.47 (16944) hydrogen bonds : bond 0.13231 / 13.74 ( 384) hydrogen bonds : angle 3.40737 / 4.42 ( 709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.167 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 23 average time/residue: 0.1125 time to fit residues: 3.6127 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 50.0000 chunk 12 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.074222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044322 restraints weight = 63789.974| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.15 r_work: 0.2754 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11000 Z= 0.187 Angle : 0.721 27.900 16944 Z= 0.372 Chirality : 0.071 1.929 2221 Planarity : 0.005 0.020 581 Dihedral : 26.055 174.052 6649 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.04 % Allowed : 29.29 % Favored : 66.67 % 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: -1.40 (0.89), residues: 114 helix: 1.08 (0.80), residues: 47 sheet: -3.11 (0.85), residues: 26 loop : -1.66 (1.25), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.008 0.002 TYR B 5 PHE 0.013 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.19 (11000) covalent geometry : angle 0.72082 / 0.37 (16944) hydrogen bonds : bond 0.10392 / 10.76 ( 384) hydrogen bonds : angle 3.14904 / 4.05 ( 709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.155 Fit side-chains REVERT: B 15 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8430 (tm-30) outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.0952 time to fit residues: 3.1559 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 17 optimal weight: 50.0000 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.073661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.043548 restraints weight = 64254.619| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.30 r_work: 0.2730 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11000 Z= 0.281 Angle : 0.798 28.167 16944 Z= 0.400 Chirality : 0.075 1.892 2221 Planarity : 0.005 0.024 581 Dihedral : 25.959 174.828 6649 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.05 % Allowed : 31.31 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.88), residues: 114 helix: 0.74 (0.79), residues: 46 sheet: -2.80 (0.91), residues: 26 loop : -1.65 (1.22), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 42 TYR 0.013 0.002 TYR B 5 PHE 0.007 0.002 PHE B 28 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.28 (11000) covalent geometry : angle 0.79816 / 0.40 (16944) hydrogen bonds : bond 0.10927 / 11.39 ( 384) hydrogen bonds : angle 3.12285 / 4.02 ( 709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.141 Fit side-chains REVERT: B 15 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8339 (tm-30) outliers start: 5 outliers final: 4 residues processed: 18 average time/residue: 0.0982 time to fit residues: 2.6307 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 39 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.074103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.044268 restraints weight = 63687.682| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.21 r_work: 0.2757 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11000 Z= 0.214 Angle : 0.727 27.970 16944 Z= 0.368 Chirality : 0.071 1.914 2221 Planarity : 0.005 0.023 581 Dihedral : 25.911 174.114 6649 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 3.03 % Allowed : 33.33 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.89), residues: 114 helix: 1.03 (0.80), residues: 47 sheet: -2.73 (0.94), residues: 26 loop : -1.57 (1.22), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 86 TYR 0.010 0.002 TYR B 5 PHE 0.010 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.21 (11000) covalent geometry : angle 0.72693 / 0.37 (16944) hydrogen bonds : bond 0.09932 / 10.36 ( 384) hydrogen bonds : angle 2.99681 / 3.84 ( 709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.149 Fit side-chains REVERT: B 15 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8326 (tm-30) outliers start: 3 outliers final: 1 residues processed: 18 average time/residue: 0.1028 time to fit residues: 2.7134 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 50.0000 chunk 17 optimal weight: 50.0000 chunk 37 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 overall best weight: 5.1992 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.073066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.042954 restraints weight = 63456.258| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.57 r_work: 0.2706 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11000 Z= 0.372 Angle : 0.893 28.993 16944 Z= 0.439 Chirality : 0.078 1.866 2221 Planarity : 0.006 0.028 581 Dihedral : 26.013 175.367 6645 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 27.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 5.05 % Allowed : 31.31 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.87), residues: 114 helix: 0.40 (0.77), residues: 46 sheet: -2.67 (0.97), residues: 26 loop : -1.41 (1.22), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 65 TYR 0.019 0.003 TYR B 5 PHE 0.009 0.002 PHE B 28 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.37 (11000) covalent geometry : angle 0.89254 / 0.44 (16944) hydrogen bonds : bond 0.12031 / 12.66 ( 384) hydrogen bonds : angle 3.14635 / 4.00 ( 709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.104 Fit side-chains REVERT: B 15 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8205 (tm-30) REVERT: B 19 GLN cc_start: 0.8618 (mp10) cc_final: 0.8335 (mp10) outliers start: 5 outliers final: 5 residues processed: 20 average time/residue: 0.0811 time to fit residues: 2.3719 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 15 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.071983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.041735 restraints weight = 64107.053| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.47 r_work: 0.2663 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 11000 Z= 0.538 Angle : 1.159 30.070 16944 Z= 0.556 Chirality : 0.090 1.819 2221 Planarity : 0.007 0.052 581 Dihedral : 26.330 173.637 6645 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 38.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 6.06 % Allowed : 32.32 % Favored : 61.62 % 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: -2.24 (0.83), residues: 114 helix: -0.28 (0.74), residues: 46 sheet: -2.89 (0.96), residues: 26 loop : -1.68 (1.16), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.029 0.005 TYR B 5 PHE 0.014 0.004 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00848 / 0.54 (11000) covalent geometry : angle 1.15871 / 0.56 (16944) hydrogen bonds : bond 0.15561 / 16.38 ( 384) hydrogen bonds : angle 3.48283 / 4.41 ( 709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.186 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 17 average time/residue: 0.0950 time to fit residues: 2.5302 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 40.0000 chunk 21 optimal weight: 50.0000 chunk 41 optimal weight: 0.0770 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.073268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.043766 restraints weight = 62796.390| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.27 r_work: 0.2725 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11000 Z= 0.238 Angle : 0.786 28.494 16944 Z= 0.400 Chirality : 0.074 1.930 2221 Planarity : 0.005 0.028 581 Dihedral : 26.169 170.282 6645 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 5.05 % Allowed : 34.34 % Favored : 60.61 % 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 (0.87), residues: 114 helix: 0.50 (0.79), residues: 47 sheet: -2.99 (0.95), residues: 26 loop : -1.80 (1.20), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 65 TYR 0.013 0.002 TYR B 31 PHE 0.014 0.002 PHE B 68 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.24 (11000) covalent geometry : angle 0.78556 / 0.40 (16944) hydrogen bonds : bond 0.10982 / 11.63 ( 384) hydrogen bonds : angle 3.10719 / 3.94 ( 709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.155 Fit side-chains REVERT: B 15 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 19 GLN cc_start: 0.8619 (mp10) cc_final: 0.8304 (mp10) outliers start: 5 outliers final: 5 residues processed: 19 average time/residue: 0.0929 time to fit residues: 2.6875 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 50.0000 chunk 16 optimal weight: 50.0000 chunk 14 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 50.0000 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.073422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043373 restraints weight = 64203.549| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.26 r_work: 0.2729 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11000 Z= 0.236 Angle : 0.758 28.113 16944 Z= 0.380 Chirality : 0.073 1.929 2221 Planarity : 0.005 0.030 581 Dihedral : 25.898 171.950 6645 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.05 % Allowed : 36.36 % Favored : 58.59 % 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: -1.52 (0.88), residues: 114 helix: 0.59 (0.80), residues: 47 sheet: -2.78 (0.97), residues: 26 loop : -1.51 (1.19), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.011 0.002 TYR B 5 PHE 0.008 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.24 (11000) covalent geometry : angle 0.75827 / 0.38 (16944) hydrogen bonds : bond 0.10133 / 10.69 ( 384) hydrogen bonds : angle 2.98966 / 3.82 ( 709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3266.67 seconds wall clock time: 56 minutes 30.91 seconds (3390.91 seconds total)