Starting phenix.real_space_refine on Thu Jul 2 19:50:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zib_74268/07_2026/9zib_74268.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zib_74268/07_2026/9zib_74268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zib_74268/07_2026/9zib_74268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zib_74268/07_2026/9zib_74268.map" model { file = "/net/cci-nas-00/data/ceres_data/9zib_74268/07_2026/9zib_74268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zib_74268/07_2026/9zib_74268.cif" } resolution = 3.1 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= 0.007 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 41 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 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9950 Number of models: 1 Model: "" Number of chains: 4 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} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.19, per 1000 atoms: 0.22 Number of scatterers: 9950 At special positions: 0 Unit cell: (108.336, 168.36, 149.328, 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 41 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: 0.77 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: 6 helices and 1 sheets defined 51.7% alpha, 14.7% beta 125 base pairs and 194 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.786A pdb=" N ARG B 6 " --> pdb=" O LYS B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.522A pdb=" N PHE B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 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 21 through 24 49 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 320 hydrogen bonds 534 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 194 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.06 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: 1094 1.33 - 1.45: 5234 1.45 - 1.57: 3834 1.57 - 1.68: 833 1.68 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N7 G A 372 " pdb=" C5 G A 372 " ideal model delta sigma weight residual 1.388 1.373 0.015 6.00e-03 2.78e+04 6.00e+00 bond pdb=" C8 G A 372 " pdb=" N7 G A 372 " ideal model delta sigma weight residual 1.305 1.291 0.014 6.00e-03 2.78e+04 5.30e+00 bond pdb=" C6 G A 317 " pdb=" O6 G A 317 " ideal model delta sigma weight residual 1.237 1.217 0.020 9.00e-03 1.23e+04 4.80e+00 bond pdb=" N9 A A 155 " pdb=" C4 A A 155 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.36e+00 bond pdb=" C5 G A 317 " pdb=" C6 G A 317 " ideal model delta sigma weight residual 1.419 1.399 0.020 1.00e-02 1.00e+04 4.01e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 16474 1.66 - 3.32: 377 3.32 - 4.98: 74 4.98 - 6.65: 17 6.65 - 8.31: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O2 C A 36 " pdb=" C2 C A 36 " pdb=" N3 C A 36 " ideal model delta sigma weight residual 121.90 118.37 3.53 7.00e-01 2.04e+00 2.54e+01 angle pdb=" C5 G A 317 " pdb=" C6 G A 317 " pdb=" O6 G A 317 " ideal model delta sigma weight residual 128.60 125.60 3.00 6.00e-01 2.78e+00 2.51e+01 angle pdb=" O3' U A 371 " pdb=" C3' U A 371 " pdb=" C2' U A 371 " ideal model delta sigma weight residual 109.50 116.67 -7.17 1.50e+00 4.44e-01 2.28e+01 angle pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sigma weight residual 117.70 122.95 -5.25 1.20e+00 6.94e-01 1.92e+01 angle pdb=" N9 G A 317 " pdb=" C4 G A 317 " pdb=" C5 G A 317 " ideal model delta sigma weight residual 105.40 103.69 1.71 4.00e-01 6.25e+00 1.83e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 5943 35.73 - 71.45: 1017 71.45 - 107.18: 136 107.18 - 142.90: 7 142.90 - 178.63: 13 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: 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 200.00 25.98 174.02 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' C A 207 " pdb=" C1' C A 207 " pdb=" N1 C A 207 " pdb=" C2 C A 207 " ideal model delta sinusoidal sigma weight residual 200.00 50.41 149.59 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' C A 219 " pdb=" C1' C A 219 " pdb=" N1 C A 219 " pdb=" C2 C A 219 " ideal model delta sinusoidal sigma weight residual -128.00 50.63 -178.63 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2113 0.071 - 0.142: 86 0.142 - 0.214: 16 0.214 - 0.285: 5 0.285 - 0.356: 1 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C3' U A 371 " pdb=" C4' U A 371 " pdb=" O3' U A 371 " pdb=" C2' U A 371 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C3' U A 185 " pdb=" C4' U A 185 " pdb=" O3' U A 185 " pdb=" C2' U A 185 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1' U A 371 " pdb=" O4' U A 371 " pdb=" C2' U A 371 " pdb=" N1 U A 371 " both_signs ideal model delta sigma weight residual False 2.45 2.22 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 317 " 0.037 2.00e-02 2.50e+03 1.70e-02 8.70e+00 pdb=" N9 G A 317 " -0.043 2.00e-02 2.50e+03 pdb=" C8 G A 317 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 317 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 317 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G A 317 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A 317 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G A 317 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G A 317 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G A 317 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G A 317 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G A 317 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 318 " -0.037 2.00e-02 2.50e+03 1.82e-02 7.48e+00 pdb=" N1 C A 318 " 0.035 2.00e-02 2.50e+03 pdb=" C2 C A 318 " 0.008 2.00e-02 2.50e+03 pdb=" O2 C A 318 " 0.006 2.00e-02 2.50e+03 pdb=" N3 C A 318 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C A 318 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C A 318 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C A 318 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C A 318 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.031 2.00e-02 2.50e+03 1.33e-02 5.34e+00 pdb=" N9 G A 298 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.006 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 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.003 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 44 2.52 - 3.12: 6856 3.12 - 3.71: 20615 3.71 - 4.31: 27479 4.31 - 4.90: 35516 Nonbonded interactions: 90510 Sorted by model distance: nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 508 " model vdw 1.927 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 511 " model vdw 1.986 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 511 " model vdw 2.027 2.170 nonbonded pdb=" O2' A A 277 " pdb="MG MG A 511 " model vdw 2.028 2.170 nonbonded pdb=" N7 G A 388 " pdb="MG MG A 531 " model vdw 2.034 2.250 ... (remaining 90505 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: 7.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 10.510 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 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 0.031 11000 Z= 0.286 Angle : 0.633 8.307 16944 Z= 0.578 Chirality : 0.035 0.356 2221 Planarity : 0.004 0.018 581 Dihedral : 26.661 178.631 6900 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % 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: 0.48 (0.88), residues: 114 helix: 2.10 (0.78), residues: 48 sheet: -0.13 (1.24), residues: 24 loop : -1.56 (1.09), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 86 TYR 0.005 0.001 TYR B 94 PHE 0.004 0.001 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.29 (11000) covalent geometry : angle 0.63253 / 0.58 (16944) hydrogen bonds : bond 0.11893 / 11.38 ( 369) hydrogen bonds : angle 2.97926 / 3.28 ( 666) *********************** 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.142 Fit side-chains REVERT: B 19 GLN cc_start: 0.8832 (pt0) cc_final: 0.8564 (pt0) outliers start: 3 outliers final: 3 residues processed: 28 average time/residue: 0.0951 time to fit residues: 3.8281 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 51 LEU 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: 2.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.095437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.052413 restraints weight = 48718.761| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.56 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 11000 Z= 0.478 Angle : 0.733 10.933 16944 Z= 0.436 Chirality : 0.051 0.268 2221 Planarity : 0.006 0.028 581 Dihedral : 26.904 179.896 6651 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 10.10 % Allowed : 25.25 % 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: 0.06 (0.86), residues: 114 helix: 1.53 (0.75), residues: 54 sheet: -0.85 (1.07), residues: 26 loop : -1.59 (1.17), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 6 TYR 0.019 0.003 TYR B 81 PHE 0.015 0.003 PHE B 13 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.48 (11000) covalent geometry : angle 0.73343 / 0.44 (16944) hydrogen bonds : bond 0.11509 / 11.96 ( 369) hydrogen bonds : angle 2.61647 / 2.96 ( 666) *********************** 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.143 Fit side-chains REVERT: B 83 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9126 (mm) outliers start: 10 outliers final: 5 residues processed: 30 average time/residue: 0.0936 time to fit residues: 4.0082 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 50.0000 chunk 30 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.096062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053693 restraints weight = 48229.562| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.40 r_work: 0.2705 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11000 Z= 0.289 Angle : 0.586 9.041 16944 Z= 0.363 Chirality : 0.041 0.265 2221 Planarity : 0.005 0.019 581 Dihedral : 26.971 179.783 6650 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 6.06 % Allowed : 27.27 % 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: 0.32 (0.87), residues: 114 helix: 1.90 (0.78), residues: 54 sheet: -0.98 (1.04), residues: 26 loop : -1.54 (1.14), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 6 TYR 0.009 0.002 TYR B 31 PHE 0.010 0.002 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.29 (11000) covalent geometry : angle 0.58631 / 0.36 (16944) hydrogen bonds : bond 0.10030 / 10.86 ( 369) hydrogen bonds : angle 2.36787 / 2.72 ( 666) *********************** 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.175 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 28 average time/residue: 0.0802 time to fit residues: 3.4362 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.095160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.054547 restraints weight = 48940.467| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.74 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11000 Z= 0.357 Angle : 0.652 10.998 16944 Z= 0.399 Chirality : 0.045 0.269 2221 Planarity : 0.005 0.024 581 Dihedral : 27.087 179.916 6650 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 9.09 % Allowed : 27.27 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.87), residues: 114 helix: 1.61 (0.77), residues: 54 sheet: -1.21 (1.02), residues: 26 loop : -1.31 (1.21), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 6 TYR 0.012 0.002 TYR B 81 PHE 0.010 0.002 PHE B 13 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.36 (11000) covalent geometry : angle 0.65166 / 0.40 (16944) hydrogen bonds : bond 0.11080 / 11.67 ( 369) hydrogen bonds : angle 2.42668 / 2.69 ( 666) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.139 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 28 average time/residue: 0.0842 time to fit residues: 3.5017 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS 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 22 optimal weight: 50.0000 chunk 12 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.094543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.053120 restraints weight = 48619.388| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.56 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11000 Z= 0.412 Angle : 0.671 11.777 16944 Z= 0.410 Chirality : 0.049 0.279 2221 Planarity : 0.005 0.029 581 Dihedral : 27.217 179.701 6650 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % 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: 0.12 (0.87), residues: 114 helix: 1.83 (0.77), residues: 54 sheet: -1.49 (1.00), residues: 26 loop : -1.42 (1.22), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.009 0.002 TYR B 31 PHE 0.013 0.003 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.41 (11000) covalent geometry : angle 0.67111 / 0.41 (16944) hydrogen bonds : bond 0.11437 / 11.97 ( 369) hydrogen bonds : angle 2.55564 / 2.86 ( 666) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.107 Fit side-chains REVERT: B 83 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9177 (mm) outliers start: 7 outliers final: 5 residues processed: 27 average time/residue: 0.0872 time to fit residues: 3.5310 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 83 ILE 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 6 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 50.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.094544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.055815 restraints weight = 48985.235| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.33 r_work: 0.2645 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2857 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= 0.377 Angle : 0.645 10.585 16944 Z= 0.397 Chirality : 0.046 0.284 2221 Planarity : 0.005 0.040 581 Dihedral : 27.175 179.976 6650 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 8.08 % Allowed : 29.29 % 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: 0.02 (0.88), residues: 114 helix: 1.70 (0.77), residues: 54 sheet: -1.34 (1.03), residues: 26 loop : -1.56 (1.22), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 35 TYR 0.007 0.002 TYR B 81 PHE 0.012 0.002 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.38 (11000) covalent geometry : angle 0.64539 / 0.40 (16944) hydrogen bonds : bond 0.10936 / 11.51 ( 369) hydrogen bonds : angle 2.43014 / 2.70 ( 666) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.150 Fit side-chains REVERT: B 12 GLU cc_start: 0.9217 (mt-10) cc_final: 0.9008 (mt-10) outliers start: 8 outliers final: 6 residues processed: 25 average time/residue: 0.0882 time to fit residues: 3.2914 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.095616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.059765 restraints weight = 48814.128| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.44 r_work: 0.2706 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11000 Z= 0.201 Angle : 0.550 8.892 16944 Z= 0.346 Chirality : 0.040 0.283 2221 Planarity : 0.005 0.036 581 Dihedral : 27.081 179.761 6650 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 5.05 % Allowed : 32.32 % 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: 0.41 (0.89), residues: 114 helix: 2.01 (0.79), residues: 54 sheet: -1.17 (1.04), residues: 26 loop : -1.34 (1.22), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 57 TYR 0.007 0.001 TYR B 94 PHE 0.007 0.001 PHE B 13 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.20 (11000) covalent geometry : angle 0.55041 / 0.35 (16944) hydrogen bonds : bond 0.09660 / 10.67 ( 369) hydrogen bonds : angle 2.28726 / 2.58 ( 666) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.137 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 27 average time/residue: 0.0835 time to fit residues: 3.3885 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 50.0000 chunk 21 optimal weight: 50.0000 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.093898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.052604 restraints weight = 48354.141| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.80 r_work: 0.2629 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 11000 Z= 0.485 Angle : 0.714 7.624 16944 Z= 0.429 Chirality : 0.052 0.285 2221 Planarity : 0.006 0.026 581 Dihedral : 27.087 179.889 6650 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 6.06 % Allowed : 28.28 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.87), residues: 114 helix: 1.60 (0.75), residues: 54 sheet: -1.33 (1.02), residues: 26 loop : -1.55 (1.24), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.012 0.002 TYR B 81 PHE 0.011 0.002 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00808 / 0.49 (11000) covalent geometry : angle 0.71378 / 0.43 (16944) hydrogen bonds : bond 0.11662 / 12.17 ( 369) hydrogen bonds : angle 2.51726 / 2.81 ( 666) *********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.200 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 25 average time/residue: 0.0871 time to fit residues: 3.3212 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.095385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053420 restraints weight = 48661.210| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.87 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11000 Z= 0.202 Angle : 0.546 6.956 16944 Z= 0.346 Chirality : 0.040 0.287 2221 Planarity : 0.004 0.024 581 Dihedral : 27.088 179.754 6650 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.04 % Allowed : 32.32 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.89), residues: 114 helix: 2.01 (0.78), residues: 54 sheet: -1.24 (1.03), residues: 26 loop : -1.39 (1.23), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 57 TYR 0.007 0.001 TYR B 81 PHE 0.006 0.001 PHE B 13 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.20 (11000) covalent geometry : angle 0.54628 / 0.35 (16944) hydrogen bonds : bond 0.09803 / 10.77 ( 369) hydrogen bonds : angle 2.30065 / 2.61 ( 666) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.110 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.0831 time to fit residues: 3.2561 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 50.0000 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.094328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.052583 restraints weight = 48169.399| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.17 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11000 Z= 0.368 Angle : 0.625 7.283 16944 Z= 0.386 Chirality : 0.046 0.285 2221 Planarity : 0.005 0.024 581 Dihedral : 27.065 179.898 6650 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 4.04 % Allowed : 30.30 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.87), residues: 114 helix: 1.83 (0.77), residues: 54 sheet: -1.28 (1.02), residues: 26 loop : -1.54 (1.22), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 65 TYR 0.009 0.002 TYR B 81 PHE 0.008 0.002 PHE B 13 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.37 (11000) covalent geometry : angle 0.62485 / 0.39 (16944) hydrogen bonds : bond 0.10862 / 11.55 ( 369) hydrogen bonds : angle 2.41488 / 2.70 ( 666) ********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.141 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 23 average time/residue: 0.0881 time to fit residues: 2.9625 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 16 optimal weight: 50.0000 chunk 17 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 overall best weight: 6.3190 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.093046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.051374 restraints weight = 48664.593| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.86 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 11000 Z= 0.561 Angle : 0.782 8.122 16944 Z= 0.468 Chirality : 0.055 0.312 2221 Planarity : 0.007 0.044 581 Dihedral : 27.223 179.880 6650 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 6.06 % Allowed : 29.29 % 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: -0.46 (0.86), residues: 114 helix: 1.38 (0.73), residues: 54 sheet: -1.56 (1.01), residues: 26 loop : -1.95 (1.26), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 65 TYR 0.009 0.002 TYR B 81 PHE 0.010 0.002 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00946 / 0.56 (11000) covalent geometry : angle 0.78156 / 0.47 (16944) hydrogen bonds : bond 0.13460 / 13.49 ( 369) hydrogen bonds : angle 2.70281 / 3.04 ( 666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.15 seconds wall clock time: 56 minutes 45.28 seconds (3405.28 seconds total)