Starting phenix.real_space_refine on Wed Aug 5 13:24:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zig_74273/08_2026/9zig_74273.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zig_74273/08_2026/9zig_74273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zig_74273/08_2026/9zig_74273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zig_74273/08_2026/9zig_74273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zig_74273/08_2026/9zig_74273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zig_74273/08_2026/9zig_74273.map" } resolution = 3.44 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 30 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 4 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: 9939 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': 23, 'rna2p_pyr': 15, 'rna3p_pur': 220, 'rna3p_pyr': 159} Link IDs: {'rna2p': 38, 'rna3p': 378} 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Unusual residues: {' MG': 30} Classifications: {'undetermined': 30} Link IDs: {None: 29} Time building chain proxies: 2.49, per 1000 atoms: 0.25 Number of scatterers: 9939 At special positions: 0 Unit cell: (124.44, 172.02, 147.864, 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 30 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: 0.81 Conformation dependent library (CDL) restraints added in 70.5 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: 4 helices and 1 sheets defined 44.8% alpha, 14.7% beta 137 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.669A pdb=" N GLU B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.501A pdb=" N THR B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) 47 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 616 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.07 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: 1078 1.33 - 1.45: 5279 1.45 - 1.57: 3805 1.57 - 1.69: 833 1.69 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 261 " pdb=" C4 A A 261 " ideal model delta sigma weight residual 1.374 1.363 0.011 6.00e-03 2.78e+04 3.21e+00 bond pdb=" N7 A A 332 " pdb=" C5 A A 332 " ideal model delta sigma weight residual 1.388 1.379 0.009 6.00e-03 2.78e+04 2.06e+00 bond pdb=" O3' G A 32 " pdb=" P U A 33 " ideal model delta sigma weight residual 1.607 1.624 -0.017 1.20e-02 6.94e+03 1.99e+00 bond pdb=" N9 A A 189 " pdb=" C4 A A 189 " ideal model delta sigma weight residual 1.374 1.382 -0.008 6.00e-03 2.78e+04 1.97e+00 bond pdb=" N1 U A 267 " pdb=" C2 U A 267 " ideal model delta sigma weight residual 1.381 1.393 -0.012 9.00e-03 1.23e+04 1.78e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 15923 2.19 - 4.38: 1000 4.38 - 6.58: 17 6.58 - 8.77: 3 8.77 - 10.96: 1 Bond angle restraints: 16944 Sorted by residual: angle pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C6 C A 318 " ideal model delta sigma weight residual 120.80 127.68 -6.88 1.20e+00 6.94e-01 3.29e+01 angle pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sigma weight residual 118.80 112.75 6.05 1.10e+00 8.26e-01 3.02e+01 angle pdb=" O4' G A 32 " pdb=" C1' G A 32 " pdb=" N9 G A 32 " ideal model delta sigma weight residual 108.20 103.86 4.34 8.00e-01 1.56e+00 2.95e+01 angle pdb=" C3' G A 32 " pdb=" O3' G A 32 " pdb=" P U A 33 " ideal model delta sigma weight residual 119.70 125.71 -6.01 1.20e+00 6.94e-01 2.51e+01 angle pdb=" N1 C A 318 " pdb=" C2 C A 318 " pdb=" O2 C A 318 " ideal model delta sigma weight residual 118.90 115.99 2.91 6.00e-01 2.78e+00 2.36e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 6010 35.28 - 70.55: 960 70.55 - 105.83: 137 105.83 - 141.10: 6 141.10 - 176.38: 3 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 -160.00 16.38 -176.38 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A 371 " pdb=" C1' U A 371 " pdb=" N1 U A 371 " pdb=" C2 U A 371 " ideal model delta sinusoidal sigma weight residual -160.00 -28.36 -131.64 1 1.50e+01 4.44e-03 7.10e+01 dihedral pdb=" O4' C A 318 " pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sinusoidal sigma weight residual -160.00 -91.72 -68.28 1 1.50e+01 4.44e-03 2.69e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1565 0.045 - 0.089: 223 0.089 - 0.133: 278 0.133 - 0.178: 148 0.178 - 0.222: 7 Chirality restraints: 2221 Sorted by residual: chirality pdb=" P U A 33 " pdb=" OP1 U A 33 " pdb=" OP2 U A 33 " pdb=" O5' U A 33 " both_signs ideal model delta sigma weight residual True 2.41 -2.63 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' U A 171 " pdb=" C4' U A 171 " pdb=" O3' U A 171 " pdb=" C2' U A 171 " both_signs ideal model delta sigma weight residual False -2.48 -2.26 -0.22 2.00e-01 2.50e+01 1.24e+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 -2.26 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 32 " -0.040 2.00e-02 2.50e+03 1.76e-02 9.31e+00 pdb=" N9 G A 32 " 0.043 2.00e-02 2.50e+03 pdb=" C8 G A 32 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G A 32 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G A 32 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A 32 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G A 32 " -0.013 2.00e-02 2.50e+03 pdb=" N1 G A 32 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G A 32 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A 32 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A 32 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A 32 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.032 2.00e-02 2.50e+03 1.42e-02 6.09e+00 pdb=" N9 G A 298 " -0.036 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 332 " -0.033 2.00e-02 2.50e+03 1.45e-02 5.78e+00 pdb=" N9 A A 332 " 0.031 2.00e-02 2.50e+03 pdb=" C8 A A 332 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 332 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A A 332 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 332 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A A 332 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A A 332 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A A 332 " 0.005 2.00e-02 2.50e+03 pdb=" N3 A A 332 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A A 332 " 0.005 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 40 2.55 - 3.14: 7273 3.14 - 3.72: 21834 3.72 - 4.31: 27797 4.31 - 4.90: 34484 Nonbonded interactions: 91428 Sorted by model distance: nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 507 " model vdw 1.960 2.170 nonbonded pdb=" OP2 U A 393 " pdb="MG MG A 528 " model vdw 1.974 2.170 nonbonded pdb=" O2' A A 277 " pdb="MG MG A 510 " model vdw 1.983 2.170 nonbonded pdb=" OP2 C A 258 " pdb="MG MG A 507 " model vdw 1.984 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 510 " model vdw 1.991 2.170 ... (remaining 91423 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: 10.110 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: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 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 0.039 11000 Z= 0.271 Angle : 0.850 10.961 16944 Z= 0.717 Chirality : 0.064 0.222 2221 Planarity : 0.004 0.024 581 Dihedral : 25.274 176.377 6900 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.03 % Allowed : 24.24 % Favored : 72.73 % 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: -1.10 (0.80), residues: 114 helix: 0.92 (0.80), residues: 46 sheet: 0.08 (1.10), residues: 24 loop : -3.12 (0.83), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 106 TYR 0.008 0.001 TYR B 94 PHE 0.005 0.001 PHE B 13 HIS 0.011 0.007 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.27 (11000) covalent geometry : angle 0.85025 / 0.72 (16944) hydrogen bonds : bond 0.09657 / 10.49 ( 398) hydrogen bonds : angle 4.07133 / 5.01 ( 748) *********************** 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 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: B 12 GLU cc_start: 0.8727 (mt-10) cc_final: 0.7763 (mp0) REVERT: B 14 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8385 (mm-40) REVERT: B 46 SER cc_start: 0.9171 (t) cc_final: 0.8723 (p) REVERT: B 96 GLU cc_start: 0.8811 (pm20) cc_final: 0.8588 (pm20) REVERT: B 107 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8360 (mptt) REVERT: B 111 LEU cc_start: 0.8999 (mm) cc_final: 0.7915 (tt) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.1091 time to fit residues: 4.6185 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 84 ILE 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: 3.9990 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.066286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036976 restraints weight = 75807.308| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.59 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 11000 Z= 0.477 Angle : 0.950 13.653 16944 Z= 0.474 Chirality : 0.065 0.386 2221 Planarity : 0.007 0.025 581 Dihedral : 25.511 176.981 6649 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 33.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 8.08 % Allowed : 25.25 % 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: -2.03 (0.76), residues: 114 helix: -0.47 (0.71), residues: 47 sheet: 0.04 (1.26), residues: 22 loop : -3.05 (0.82), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 106 TYR 0.012 0.002 TYR B 94 PHE 0.037 0.004 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.48 (11000) covalent geometry : angle 0.95000 / 0.47 (16944) hydrogen bonds : bond 0.13879 / 14.45 ( 398) hydrogen bonds : angle 3.51235 / 4.35 ( 748) *********************** 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 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.143 Fit side-chains REVERT: B 12 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8060 (mp0) REVERT: B 14 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8330 (mm-40) REVERT: B 46 SER cc_start: 0.9157 (t) cc_final: 0.8910 (m) REVERT: B 107 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8397 (mptt) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.1234 time to fit residues: 6.1081 Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.065673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.037204 restraints weight = 76956.823| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.34 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 11000 Z= 0.497 Angle : 1.014 13.681 16944 Z= 0.509 Chirality : 0.068 0.411 2221 Planarity : 0.007 0.041 581 Dihedral : 26.098 175.272 6649 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 41.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % 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: -2.43 (0.77), residues: 114 helix: -0.54 (0.74), residues: 47 sheet: -0.86 (1.06), residues: 26 loop : -3.38 (0.88), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.020 0.002 TYR B 94 PHE 0.037 0.005 PHE B 28 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.50 (11000) covalent geometry : angle 1.01392 / 0.51 (16944) hydrogen bonds : bond 0.14492 / 15.09 ( 398) hydrogen bonds : angle 3.74609 / 4.87 ( 748) *********************** 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 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.145 Fit side-chains REVERT: B 12 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8174 (mp0) REVERT: B 13 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6902 (m-10) REVERT: B 14 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8233 (mm-40) REVERT: B 46 SER cc_start: 0.9195 (t) cc_final: 0.8699 (p) REVERT: B 51 LEU cc_start: 0.9263 (mp) cc_final: 0.9057 (mp) REVERT: B 107 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8363 (mmtt) outliers start: 7 outliers final: 4 residues processed: 34 average time/residue: 0.1128 time to fit residues: 5.2180 Evaluate side-chains 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 30.0000 chunk 21 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.066064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.037596 restraints weight = 76634.435| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.84 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11000 Z= 0.323 Angle : 0.755 11.073 16944 Z= 0.405 Chirality : 0.051 0.368 2221 Planarity : 0.006 0.042 581 Dihedral : 26.017 174.641 6649 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 31.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 7.07 % Allowed : 25.25 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.78), residues: 114 helix: -0.18 (0.75), residues: 47 sheet: -0.71 (1.07), residues: 26 loop : -3.44 (0.87), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.009 0.001 TYR B 31 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 0.00480 / 0.32 (11000) covalent geometry : angle 0.75508 / 0.41 (16944) hydrogen bonds : bond 0.11949 / 12.19 ( 398) hydrogen bonds : angle 3.32381 / 4.26 ( 748) *********************** 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 40 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.185 Fit side-chains REVERT: B 12 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: B 13 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6940 (m-10) REVERT: B 14 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8239 (mm-40) REVERT: B 46 SER cc_start: 0.9126 (t) cc_final: 0.8502 (p) REVERT: B 103 HIS cc_start: 0.8851 (t70) cc_final: 0.8472 (t-170) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.1060 time to fit residues: 5.4466 Evaluate side-chains 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 overall best weight: 9.9990 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.064895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.036762 restraints weight = 77433.314| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.62 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 11000 Z= 0.602 Angle : 1.163 15.842 16944 Z= 0.569 Chirality : 0.076 0.436 2221 Planarity : 0.007 0.049 581 Dihedral : 26.263 174.491 6649 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 51.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 9.09 % Allowed : 24.24 % 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: -2.92 (0.74), residues: 114 helix: -0.91 (0.70), residues: 47 sheet: -0.91 (1.24), residues: 21 loop : -3.57 (0.78), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 106 TYR 0.008 0.002 TYR B 94 PHE 0.020 0.003 PHE B 13 HIS 0.015 0.010 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00899 / 0.60 (11000) covalent geometry : angle 1.16322 / 0.57 (16944) hydrogen bonds : bond 0.16736 / 17.72 ( 398) hydrogen bonds : angle 3.95694 / 5.13 ( 748) *********************** 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 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: B 12 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: B 13 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6887 (m-10) REVERT: B 14 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8339 (mm-40) REVERT: B 46 SER cc_start: 0.9171 (t) cc_final: 0.8631 (p) outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 0.1011 time to fit residues: 4.9013 Evaluate side-chains 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 19 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 50.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.066098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.037405 restraints weight = 78312.749| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.68 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11000 Z= 0.239 Angle : 0.694 10.341 16944 Z= 0.384 Chirality : 0.047 0.341 2221 Planarity : 0.005 0.020 581 Dihedral : 26.103 176.168 6649 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 28.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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: -2.35 (0.76), residues: 114 helix: -0.27 (0.75), residues: 46 sheet: -0.58 (1.23), residues: 21 loop : -3.45 (0.76), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 59 TYR 0.006 0.001 TYR B 94 PHE 0.010 0.002 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.24 (11000) covalent geometry : angle 0.69403 / 0.38 (16944) hydrogen bonds : bond 0.11207 / 11.52 ( 398) hydrogen bonds : angle 3.27063 / 4.21 ( 748) *********************** 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 41 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.148 Fit side-chains REVERT: B 12 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: B 13 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6942 (m-10) REVERT: B 14 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8227 (mm-40) REVERT: B 46 SER cc_start: 0.9158 (t) cc_final: 0.8574 (p) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.1082 time to fit residues: 5.6473 Evaluate side-chains 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 overall best weight: 6.0788 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.065363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036828 restraints weight = 77474.986| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.02 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3699 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= 0.372 Angle : 0.825 11.387 16944 Z= 0.430 Chirality : 0.056 0.357 2221 Planarity : 0.006 0.034 581 Dihedral : 26.065 175.973 6649 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 35.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 7.07 % Allowed : 26.26 % 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: -2.69 (0.73), residues: 114 helix: -0.53 (0.73), residues: 46 sheet: -0.76 (1.21), residues: 21 loop : -3.66 (0.73), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 106 TYR 0.005 0.002 TYR B 81 PHE 0.011 0.002 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.37 (11000) covalent geometry : angle 0.82502 / 0.43 (16944) hydrogen bonds : bond 0.12847 / 13.39 ( 398) hydrogen bonds : angle 3.42927 / 4.43 ( 748) *********************** 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 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.145 Fit side-chains REVERT: B 12 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: B 13 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: B 14 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8274 (mm-40) REVERT: B 46 SER cc_start: 0.9157 (t) cc_final: 0.8607 (p) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.1039 time to fit residues: 5.1640 Evaluate side-chains 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 20 optimal weight: 50.0000 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.064565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.035224 restraints weight = 77339.254| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 4.60 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 11000 Z= 0.584 Angle : 1.163 15.762 16944 Z= 0.576 Chirality : 0.076 0.412 2221 Planarity : 0.007 0.049 581 Dihedral : 26.456 174.680 6649 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 56.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 8.08 % Allowed : 24.24 % Favored : 67.68 % 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: -3.38 (0.70), residues: 114 helix: -1.01 (0.71), residues: 47 sheet: -1.56 (1.13), residues: 21 loop : -3.93 (0.71), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 106 TYR 0.015 0.003 TYR B 63 PHE 0.018 0.003 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00863 / 0.58 (11000) covalent geometry : angle 1.16258 / 0.58 (16944) hydrogen bonds : bond 0.17960 / 19.35 ( 398) hydrogen bonds : angle 4.08227 / 5.48 ( 748) *********************** 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 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.146 Fit side-chains REVERT: B 12 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: B 13 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: B 14 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8348 (mm-40) REVERT: B 46 SER cc_start: 0.9180 (t) cc_final: 0.8612 (p) outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.1079 time to fit residues: 5.1694 Evaluate side-chains 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 30.0000 chunk 22 optimal weight: 50.0000 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.065085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.038983 restraints weight = 77449.379| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.18 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11000 Z= 0.364 Angle : 0.843 12.191 16944 Z= 0.444 Chirality : 0.057 0.339 2221 Planarity : 0.006 0.024 581 Dihedral : 26.301 176.751 6649 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 38.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 7.07 % Allowed : 26.26 % 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: -3.03 (0.72), residues: 114 helix: -0.76 (0.72), residues: 47 sheet: -1.24 (1.15), residues: 21 loop : -3.79 (0.72), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 59 TYR 0.008 0.002 TYR B 63 PHE 0.012 0.002 PHE B 13 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.36 (11000) covalent geometry : angle 0.84327 / 0.44 (16944) hydrogen bonds : bond 0.13105 / 13.97 ( 398) hydrogen bonds : angle 3.59542 / 4.78 ( 748) *********************** 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 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.117 Fit side-chains REVERT: B 1 MET cc_start: 0.7893 (mmt) cc_final: 0.7619 (mmt) REVERT: B 12 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: B 13 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6880 (m-10) REVERT: B 14 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8292 (mm-40) REVERT: B 28 PHE cc_start: 0.8840 (m-80) cc_final: 0.8537 (m-10) REVERT: B 46 SER cc_start: 0.8979 (t) cc_final: 0.8520 (p) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.0860 time to fit residues: 4.2503 Evaluate side-chains 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 39 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.064580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.035525 restraints weight = 76683.716| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 4.31 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 11000 Z= 0.509 Angle : 1.003 13.849 16944 Z= 0.507 Chirality : 0.067 0.399 2221 Planarity : 0.007 0.039 581 Dihedral : 26.373 176.108 6649 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 48.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 8.08 % Allowed : 26.26 % 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: -3.32 (0.71), residues: 114 helix: -0.97 (0.71), residues: 47 sheet: -1.56 (1.10), residues: 21 loop : -3.87 (0.73), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 106 TYR 0.008 0.002 TYR B 31 PHE 0.014 0.002 PHE B 13 HIS 0.008 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.51 (11000) covalent geometry : angle 1.00290 / 0.51 (16944) hydrogen bonds : bond 0.15280 / 16.43 ( 398) hydrogen bonds : angle 3.83128 / 5.16 ( 748) ********************** 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 40 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.144 Fit side-chains REVERT: B 1 MET cc_start: 0.7956 (mmt) cc_final: 0.7700 (mmt) REVERT: B 12 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: B 13 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6921 (m-10) REVERT: B 14 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8301 (mm-40) REVERT: B 28 PHE cc_start: 0.8841 (m-80) cc_final: 0.8536 (m-10) REVERT: B 46 SER cc_start: 0.9157 (t) cc_final: 0.8627 (p) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.1074 time to fit residues: 5.3588 Evaluate side-chains 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 40.0000 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.065754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.037164 restraints weight = 76724.447| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.53 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11000 Z= 0.203 Angle : 0.662 9.293 16944 Z= 0.373 Chirality : 0.043 0.277 2221 Planarity : 0.005 0.032 581 Dihedral : 26.189 178.963 6649 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 7.07 % Allowed : 27.27 % 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: -2.91 (0.72), residues: 114 helix: -0.51 (0.73), residues: 47 sheet: -1.32 (1.09), residues: 21 loop : -3.82 (0.73), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.007 0.002 TYR B 31 PHE 0.007 0.001 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.20 (11000) covalent geometry : angle 0.66176 / 0.37 (16944) hydrogen bonds : bond 0.10921 / 11.47 ( 398) hydrogen bonds : angle 3.19772 / 4.21 ( 748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2691.39 seconds wall clock time: 46 minutes 58.71 seconds (2818.71 seconds total)