Starting phenix.real_space_refine on Wed Aug 5 13:10:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zib_74268/08_2026/9zib_74268.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zib_74268/08_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_74268/08_2026/9zib_74268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zib_74268/08_2026/9zib_74268.map" model { file = "/net/cci-nas-00/data/ceres_data/9zib_74268/08_2026/9zib_74268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zib_74268/08_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-2.2rc3-6140/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: 2.39, per 1000 atoms: 0.24 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: 0.78 Conformation dependent library (CDL) restraints added in 67.7 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: 1.40 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: 2.30 Time building geometry restraints manager: 1.11 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=" C3' U A 371 " pdb=" C2' U A 371 " ideal model delta sigma weight residual 1.525 1.551 -0.026 1.10e-02 8.26e+03 5.47e+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 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 15384 1.66 - 3.32: 1458 3.32 - 4.98: 81 4.98 - 6.65: 19 6.65 - 8.31: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O5' G A 372 " pdb=" C5' G A 372 " pdb=" C4' G A 372 " ideal model delta sigma weight residual 109.40 114.97 -5.57 8.00e-01 1.56e+00 4.84e+01 angle pdb=" O5' A A 178 " pdb=" C5' A A 178 " pdb=" C4' A A 178 " ideal model delta sigma weight residual 109.40 113.79 -4.39 8.00e-01 1.56e+00 3.01e+01 angle pdb=" C3' C A 196 " pdb=" O3' C A 196 " pdb=" P A A 197 " ideal model delta sigma weight residual 119.70 125.83 -6.13 1.20e+00 6.94e-01 2.61e+01 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 ... (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: 1689 0.071 - 0.142: 495 0.142 - 0.214: 31 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=" C1' G A 268 " pdb=" O4' G A 268 " pdb=" C2' G A 268 " pdb=" N9 G A 268 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.45e+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 ... (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: 10.540 Set stop_for_unknowns flag: 0.010 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: 0.380 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.110 Find NCS groups from input model: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- 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= 0.318 Angle : 0.890 8.307 16944 Z= 0.762 Chirality : 0.065 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 0.00323 / 0.32 (11000) covalent geometry : angle 0.88963 / 0.76 (16944) hydrogen bonds : bond 0.11893 / 12.88 ( 369) hydrogen bonds : angle 2.97926 / 3.65 ( 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 : 0.092 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: 0.0998 time to fit residues: 3.9708 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 : 0.141 ------------------------------------------------------------------------------- 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: 10.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.9990 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.095149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.051365 restraints weight = 48511.427| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.29 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1582 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= 0.501 Angle : 0.960 10.444 16944 Z= 0.490 Chirality : 0.068 0.502 2221 Planarity : 0.006 0.032 581 Dihedral : 26.893 179.987 6651 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 11.11 % Allowed : 24.24 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.85), residues: 114 helix: 1.44 (0.74), residues: 54 sheet: -0.91 (1.07), residues: 26 loop : -1.67 (1.16), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 42 TYR 0.017 0.003 TYR B 81 PHE 0.013 0.003 PHE B 13 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.50 (11000) covalent geometry : angle 0.95962 / 0.49 (16944) hydrogen bonds : bond 0.12107 / 13.83 ( 369) hydrogen bonds : angle 2.69600 / 3.33 ( 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.150 Fit side-chains REVERT: B 2 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8187 (mtpp) REVERT: B 83 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9144 (mm) outliers start: 11 outliers final: 5 residues processed: 29 average time/residue: 0.1033 time to fit residues: 4.2766 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LYS 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: 0.7980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 10.9990 chunk 17 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 50.0000 chunk 30 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.095863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.058276 restraints weight = 48238.422| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.20 r_work: 0.2667 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11000 Z= 0.288 Angle : 0.726 10.373 16944 Z= 0.395 Chirality : 0.052 0.502 2221 Planarity : 0.005 0.021 581 Dihedral : 26.947 179.963 6650 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 17.07 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: 0.25 (0.87), residues: 114 helix: 1.87 (0.78), residues: 54 sheet: -1.13 (1.04), residues: 26 loop : -1.50 (1.16), 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 81 PHE 0.010 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.29 (11000) covalent geometry : angle 0.72594 / 0.39 (16944) hydrogen bonds : bond 0.10662 / 12.38 ( 369) hydrogen bonds : angle 2.42592 / 3.04 ( 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.146 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 28 average time/residue: 0.0999 time to fit residues: 4.0761 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 : 0.150 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.0020 chunk 26 optimal weight: 10.9990 chunk 4 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 overall best weight: 4.3996 ------------------------------------------------------------------------------- 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 = 0.094748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.051351 restraints weight = 48736.665| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.53 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2348 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= 0.388 Angle : 0.815 12.017 16944 Z= 0.435 Chirality : 0.057 0.349 2221 Planarity : 0.006 0.027 581 Dihedral : 27.024 179.493 6650 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 11.11 % Allowed : 23.23 % 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: -0.18 (0.86), residues: 114 helix: 1.45 (0.76), residues: 54 sheet: -1.32 (1.03), residues: 26 loop : -1.60 (1.19), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.011 0.002 TYR B 81 PHE 0.013 0.002 PHE B 13 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.39 (11000) covalent geometry : angle 0.81508 / 0.43 (16944) hydrogen bonds : bond 0.11902 / 13.69 ( 369) hydrogen bonds : angle 2.52695 / 3.10 ( 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.152 Fit side-chains REVERT: B 83 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9193 (mm) outliers start: 11 outliers final: 6 residues processed: 30 average time/residue: 0.0977 time to fit residues: 4.3282 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 83 ILE 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: 30.0000 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.093945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053287 restraints weight = 48604.239| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.27 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11000 Z= 0.462 Angle : 0.908 8.694 16944 Z= 0.474 Chirality : 0.064 0.348 2221 Planarity : 0.006 0.042 581 Dihedral : 27.206 179.389 6650 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % 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: -0.23 (0.86), residues: 114 helix: 1.65 (0.77), residues: 54 sheet: -1.60 (0.98), residues: 26 loop : -1.84 (1.18), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 6 TYR 0.012 0.003 TYR B 81 PHE 0.021 0.003 PHE B 13 HIS 0.009 0.006 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.46 (11000) covalent geometry : angle 0.90762 / 0.47 (16944) hydrogen bonds : bond 0.13036 / 14.68 ( 369) hydrogen bonds : angle 2.76098 / 3.36 ( 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.133 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.0918 time to fit residues: 3.3854 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 50.0000 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 14 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 50.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.094505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.052883 restraints weight = 48869.071| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.36 r_work: 0.2666 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11000 Z= 0.327 Angle : 0.732 10.036 16944 Z= 0.403 Chirality : 0.052 0.344 2221 Planarity : 0.005 0.038 581 Dihedral : 27.113 179.605 6650 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % 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: -0.06 (0.88), residues: 114 helix: 1.74 (0.78), residues: 54 sheet: -1.35 (1.03), residues: 26 loop : -1.82 (1.18), 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 81 PHE 0.012 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.33 (11000) covalent geometry : angle 0.73242 / 0.40 (16944) hydrogen bonds : bond 0.11322 / 13.09 ( 369) hydrogen bonds : angle 2.48522 / 3.10 ( 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.166 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 24 average time/residue: 0.0841 time to fit residues: 3.1021 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 : 0.164 ------------------------------------------------------------------------------- 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: 7.9990 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.095195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.053146 restraints weight = 48713.103| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.02 r_work: 0.2701 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11000 Z= 0.237 Angle : 0.629 7.662 16944 Z= 0.359 Chirality : 0.046 0.341 2221 Planarity : 0.005 0.040 581 Dihedral : 27.001 179.812 6650 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 5.05 % Allowed : 28.28 % 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: 0.17 (0.88), residues: 114 helix: 1.90 (0.78), residues: 54 sheet: -1.14 (1.04), residues: 26 loop : -1.76 (1.20), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 35 TYR 0.008 0.001 TYR B 81 PHE 0.011 0.002 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.24 (11000) covalent geometry : angle 0.62899 / 0.36 (16944) hydrogen bonds : bond 0.10169 / 12.11 ( 369) hydrogen bonds : angle 2.35390 / 2.97 ( 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.116 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 24 average time/residue: 0.0852 time to fit residues: 3.0717 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 : 0.135 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 50.0000 chunk 37 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 21 optimal weight: 50.0000 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 overall best weight: 6.2188 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.093574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.050524 restraints weight = 48167.488| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.65 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3409 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= 0.494 Angle : 0.892 8.678 16944 Z= 0.460 Chirality : 0.063 0.352 2221 Planarity : 0.006 0.029 581 Dihedral : 27.062 179.360 6650 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % 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: -0.39 (0.86), residues: 114 helix: 1.40 (0.74), residues: 54 sheet: -1.37 (1.02), residues: 26 loop : -1.99 (1.23), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 6 TYR 0.011 0.002 TYR B 81 PHE 0.014 0.003 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.49 (11000) covalent geometry : angle 0.89215 / 0.46 (16944) hydrogen bonds : bond 0.12375 / 14.15 ( 369) hydrogen bonds : angle 2.62888 / 3.23 ( 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.145 Fit side-chains REVERT: B 74 GLU cc_start: 0.8810 (mp0) cc_final: 0.8583 (mp0) outliers start: 7 outliers final: 7 residues processed: 23 average time/residue: 0.0946 time to fit residues: 3.2058 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 80 ASP 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: 6.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.095086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053988 restraints weight = 48541.987| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 0.96 r_work: 0.2699 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11000 Z= 0.202 Angle : 0.616 7.318 16944 Z= 0.357 Chirality : 0.044 0.342 2221 Planarity : 0.005 0.033 581 Dihedral : 27.031 179.726 6650 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 4.04 % Allowed : 31.31 % 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: 0.01 (0.88), residues: 114 helix: 1.91 (0.77), residues: 54 sheet: -1.29 (1.02), residues: 26 loop : -2.06 (1.20), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 86 TYR 0.009 0.001 TYR B 81 PHE 0.011 0.001 PHE B 13 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.20 (11000) covalent geometry : angle 0.61638 / 0.36 (16944) hydrogen bonds : bond 0.10368 / 12.18 ( 369) hydrogen bonds : angle 2.39043 / 3.03 ( 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.111 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.0938 time to fit residues: 3.3553 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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: 7.9990 chunk 41 optimal weight: 0.0770 chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.094050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.051076 restraints weight = 48006.430| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.37 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11000 Z= 0.374 Angle : 0.762 7.507 16944 Z= 0.408 Chirality : 0.055 0.348 2221 Planarity : 0.005 0.030 581 Dihedral : 26.969 179.503 6650 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 5.05 % Allowed : 27.27 % 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: -0.16 (0.87), residues: 114 helix: 1.73 (0.76), residues: 54 sheet: -1.36 (1.01), residues: 26 loop : -2.07 (1.20), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 65 TYR 0.011 0.002 TYR B 81 PHE 0.012 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.37 (11000) covalent geometry : angle 0.76183 / 0.41 (16944) hydrogen bonds : bond 0.11280 / 13.08 ( 369) hydrogen bonds : angle 2.48196 / 3.08 ( 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.145 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 22 average time/residue: 0.0969 time to fit residues: 3.1536 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 30.0000 chunk 16 optimal weight: 50.0000 chunk 17 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.092692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.050766 restraints weight = 48501.246| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.95 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 11000 Z= 0.570 Angle : 1.025 12.134 16944 Z= 0.513 Chirality : 0.071 0.354 2221 Planarity : 0.007 0.050 581 Dihedral : 27.153 179.176 6650 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 5.05 % Allowed : 29.29 % 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: -0.63 (0.86), residues: 114 helix: 1.34 (0.73), residues: 54 sheet: -1.50 (1.03), residues: 26 loop : -2.37 (1.21), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.012 0.003 TYR B 81 PHE 0.015 0.003 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00915 / 0.57 (11000) covalent geometry : angle 1.02466 / 0.51 (16944) hydrogen bonds : bond 0.14197 / 15.74 ( 369) hydrogen bonds : angle 2.80164 / 3.43 ( 666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3416.50 seconds wall clock time: 59 minutes 3.96 seconds (3543.96 seconds total)