Starting phenix.real_space_refine on Thu Jun 4 02:31:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zib_74268/06_2026/9zib_74268.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zib_74268/06_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_74268/06_2026/9zib_74268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zib_74268/06_2026/9zib_74268.map" model { file = "/net/cci-nas-00/data/ceres_data/9zib_74268/06_2026/9zib_74268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zib_74268/06_2026/9zib_74268.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 417 5.49 5 Mg 41 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/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: 2.35, 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: 0.74 Conformation dependent library (CDL) restraints added in 77.0 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 51.7% alpha, 14.7% beta 125 base pairs and 194 stacking pairs defined. Time for finding SS restraints: 1.76 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: 2.07 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1094 1.33 - 1.45: 5234 1.45 - 1.57: 3834 1.57 - 1.68: 833 1.68 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" C3' U A 371 " pdb=" C2' U A 371 " ideal model delta sigma weight residual 1.525 1.551 -0.026 1.50e-02 4.44e+03 2.94e+00 bond pdb=" C3' C A 196 " pdb=" O3' C A 196 " ideal model delta sigma weight residual 1.427 1.450 -0.023 1.50e-02 4.44e+03 2.26e+00 bond pdb=" O3' U A 371 " pdb=" P G A 372 " ideal model delta sigma weight residual 1.607 1.628 -0.021 1.50e-02 4.44e+03 2.03e+00 bond pdb=" C3' G A 224 " pdb=" O3' G A 224 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.50e-02 4.44e+03 1.64e+00 bond pdb=" O4' U A 371 " pdb=" C1' U A 371 " ideal model delta sigma weight residual 1.415 1.397 0.018 1.50e-02 4.44e+03 1.46e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 16474 1.66 - 3.32: 377 3.32 - 4.98: 74 4.98 - 6.65: 17 6.65 - 8.31: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O3' U A 371 " pdb=" C3' U A 371 " pdb=" C2' U A 371 " ideal model delta sigma weight residual 109.50 116.67 -7.17 1.50e+00 4.44e-01 2.28e+01 angle pdb=" C3' C A 196 " pdb=" O3' C A 196 " pdb=" P A A 197 " ideal model delta sigma weight residual 120.20 125.83 -5.63 1.50e+00 4.44e-01 1.41e+01 angle pdb=" O3' U A 185 " pdb=" C3' U A 185 " pdb=" C2' U A 185 " ideal model delta sigma weight residual 113.70 119.03 -5.33 1.50e+00 4.44e-01 1.26e+01 angle pdb=" C3' G A 224 " pdb=" O3' G A 224 " pdb=" P A A 225 " ideal model delta sigma weight residual 120.20 125.46 -5.26 1.50e+00 4.44e-01 1.23e+01 angle pdb=" O3' G A 408 " pdb=" C3' G A 408 " pdb=" C2' G A 408 " ideal model delta sigma weight residual 113.70 118.62 -4.92 1.50e+00 4.44e-01 1.07e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 5943 35.73 - 71.45: 1017 71.45 - 107.18: 136 107.18 - 142.90: 7 142.90 - 178.63: 13 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sinusoidal sigma weight residual 200.00 25.98 174.02 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' C A 207 " pdb=" C1' C A 207 " pdb=" N1 C A 207 " pdb=" C2 C A 207 " ideal model delta sinusoidal sigma weight residual 200.00 50.41 149.59 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' C A 219 " pdb=" C1' C A 219 " pdb=" N1 C A 219 " pdb=" C2 C A 219 " ideal model delta sinusoidal sigma weight residual -128.00 50.63 -178.63 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2113 0.071 - 0.142: 86 0.142 - 0.214: 16 0.214 - 0.285: 5 0.285 - 0.356: 1 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C3' U A 371 " pdb=" C4' U A 371 " pdb=" O3' U A 371 " pdb=" C2' U A 371 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C3' U A 185 " pdb=" C4' U A 185 " pdb=" O3' U A 185 " pdb=" C2' U A 185 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1' U A 371 " pdb=" O4' U A 371 " pdb=" C2' U A 371 " pdb=" N1 U A 371 " both_signs ideal model delta sigma weight residual False 2.45 2.22 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 317 " 0.037 2.00e-02 2.50e+03 1.70e-02 8.70e+00 pdb=" N9 G A 317 " -0.043 2.00e-02 2.50e+03 pdb=" C8 G A 317 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 317 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 317 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G A 317 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A 317 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G A 317 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G A 317 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G A 317 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G A 317 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G A 317 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 318 " -0.037 2.00e-02 2.50e+03 1.82e-02 7.48e+00 pdb=" N1 C A 318 " 0.035 2.00e-02 2.50e+03 pdb=" C2 C A 318 " 0.008 2.00e-02 2.50e+03 pdb=" O2 C A 318 " 0.006 2.00e-02 2.50e+03 pdb=" N3 C A 318 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C A 318 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C A 318 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C A 318 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C A 318 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.031 2.00e-02 2.50e+03 1.33e-02 5.34e+00 pdb=" N9 G A 298 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 298 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.003 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 44 2.52 - 3.12: 6856 3.12 - 3.71: 20615 3.71 - 4.31: 27479 4.31 - 4.90: 35516 Nonbonded interactions: 90510 Sorted by model distance: nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 508 " model vdw 1.927 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 511 " model vdw 1.986 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 511 " model vdw 2.027 2.170 nonbonded pdb=" O2' A A 277 " pdb="MG MG A 511 " model vdw 2.028 2.170 nonbonded pdb=" N7 G A 388 " pdb="MG MG A 531 " model vdw 2.034 2.250 ... (remaining 90505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.520 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.340 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 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= 0.159 Angle : 0.632 8.307 16944 Z= 0.326 Chirality : 0.035 0.356 2221 Planarity : 0.004 0.018 581 Dihedral : 26.661 178.631 6900 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.03 % Allowed : 33.33 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.88), residues: 114 helix: 2.10 (0.78), residues: 48 sheet: -0.13 (1.24), residues: 24 loop : -1.56 (1.09), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 86 TYR 0.005 0.001 TYR B 94 PHE 0.004 0.001 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.16 (11000) covalent geometry : angle 0.63230 / 0.33 (16944) hydrogen bonds : bond 0.11893 / 7.25 ( 369) hydrogen bonds : angle 2.97926 / 1.98 ( 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 : 0.156 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: 0.1081 time to fit residues: 4.2935 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 : 0.145 ------------------------------------------------------------------------------- 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: 6.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 40.0000 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.095438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.053819 restraints weight = 48491.854| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.59 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 11000 Z= 0.387 Angle : 0.758 9.957 16944 Z= 0.381 Chirality : 0.041 0.274 2221 Planarity : 0.005 0.019 581 Dihedral : 26.912 179.787 6651 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.05 % Allowed : 30.30 % 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: 0.40 (0.86), residues: 114 helix: 1.64 (0.76), residues: 54 sheet: -0.44 (1.10), residues: 26 loop : -1.34 (1.18), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 57 TYR 0.008 0.002 TYR B 94 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 0.00726 / 0.39 (11000) covalent geometry : angle 0.75804 / 0.38 (16944) hydrogen bonds : bond 0.09083 / 5.29 ( 369) hydrogen bonds : angle 2.13681 / 1.41 ( 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.125 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.1002 time to fit residues: 3.8025 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.096905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.055461 restraints weight = 48605.368| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.30 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11000 Z= 0.234 Angle : 0.652 11.507 16944 Z= 0.332 Chirality : 0.037 0.260 2221 Planarity : 0.004 0.020 581 Dihedral : 26.791 179.044 6650 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 6.06 % Allowed : 27.27 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.85), residues: 114 helix: 2.32 (0.77), residues: 48 sheet: -0.50 (1.07), residues: 26 loop : -1.75 (1.06), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.008 0.001 TYR B 81 PHE 0.005 0.001 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.23 (11000) covalent geometry : angle 0.65182 / 0.33 (16944) hydrogen bonds : bond 0.07751 / 4.40 ( 369) hydrogen bonds : angle 1.99062 / 1.35 ( 666) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.143 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 0.1080 time to fit residues: 3.8597 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.095043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054801 restraints weight = 49044.226| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.77 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 11000 Z= 0.348 Angle : 0.737 11.444 16944 Z= 0.372 Chirality : 0.040 0.271 2221 Planarity : 0.005 0.020 581 Dihedral : 26.903 179.721 6647 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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: 0.43 (0.86), residues: 114 helix: 1.71 (0.76), residues: 54 sheet: -0.52 (1.07), residues: 26 loop : -1.32 (1.16), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 6 TYR 0.013 0.002 TYR B 81 PHE 0.012 0.002 PHE B 13 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.35 (11000) covalent geometry : angle 0.73748 / 0.37 (16944) hydrogen bonds : bond 0.09147 / 5.35 ( 369) hydrogen bonds : angle 2.09536 / 1.38 ( 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.093 Fit side-chains REVERT: B 1 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8240 (mtp) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 0.0862 time to fit residues: 3.2579 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 : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.095607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055483 restraints weight = 48951.897| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.57 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 11000 Z= 0.291 Angle : 0.673 7.268 16944 Z= 0.343 Chirality : 0.038 0.271 2221 Planarity : 0.004 0.023 581 Dihedral : 26.820 178.609 6647 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.04 % Allowed : 29.29 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.87), residues: 114 helix: 1.87 (0.78), residues: 54 sheet: -0.57 (1.06), residues: 26 loop : -1.35 (1.19), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 26 TYR 0.008 0.001 TYR B 81 PHE 0.009 0.001 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.29 (11000) covalent geometry : angle 0.67332 / 0.34 (16944) hydrogen bonds : bond 0.08084 / 4.66 ( 369) hydrogen bonds : angle 2.01584 / 1.37 ( 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.159 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.0939 time to fit residues: 3.3047 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 17 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 21 optimal weight: 40.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.095168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053138 restraints weight = 48915.136| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.37 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 11000 Z= 0.290 Angle : 0.683 6.558 16944 Z= 0.346 Chirality : 0.038 0.268 2221 Planarity : 0.004 0.016 581 Dihedral : 26.803 178.893 6647 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.04 % Allowed : 30.30 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.88), residues: 114 helix: 1.79 (0.78), residues: 54 sheet: -0.57 (1.08), residues: 26 loop : -1.61 (1.20), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 42 TYR 0.010 0.002 TYR B 94 PHE 0.006 0.001 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.29 (11000) covalent geometry : angle 0.68281 / 0.35 (16944) hydrogen bonds : bond 0.08696 / 5.07 ( 369) hydrogen bonds : angle 2.02370 / 1.33 ( 666) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.144 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.0953 time to fit residues: 3.5135 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 chunk 37 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.095659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054087 restraints weight = 48840.647| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.36 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 11000 Z= 0.256 Angle : 0.647 6.605 16944 Z= 0.329 Chirality : 0.037 0.271 2221 Planarity : 0.004 0.017 581 Dihedral : 26.704 178.334 6647 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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: 0.58 (0.89), residues: 114 helix: 2.06 (0.77), residues: 54 sheet: -0.53 (1.08), residues: 26 loop : -1.63 (1.22), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.009 0.001 TYR B 81 PHE 0.009 0.001 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.26 (11000) covalent geometry : angle 0.64686 / 0.33 (16944) hydrogen bonds : bond 0.08076 / 4.67 ( 369) hydrogen bonds : angle 1.98564 / 1.35 ( 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.142 Fit side-chains REVERT: B 74 GLU cc_start: 0.8702 (mp0) cc_final: 0.8425 (mp0) outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 0.0818 time to fit residues: 3.0569 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 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: 20.0000 chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 40.0000 chunk 21 optimal weight: 40.0000 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.094140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054156 restraints weight = 48380.478| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.81 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 11000 Z= 0.381 Angle : 0.735 6.744 16944 Z= 0.370 Chirality : 0.041 0.279 2221 Planarity : 0.005 0.018 581 Dihedral : 26.847 178.566 6647 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 4.04 % Allowed : 35.35 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.85), residues: 114 helix: 2.33 (0.75), residues: 48 sheet: -0.90 (1.06), residues: 26 loop : -2.28 (1.05), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 6 TYR 0.008 0.002 TYR B 31 PHE 0.006 0.001 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.38 (11000) covalent geometry : angle 0.73509 / 0.37 (16944) hydrogen bonds : bond 0.09355 / 5.53 ( 369) hydrogen bonds : angle 2.09662 / 1.39 ( 666) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.143 Fit side-chains REVERT: B 74 GLU cc_start: 0.8774 (mp0) cc_final: 0.8469 (mp0) outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 0.0949 time to fit residues: 3.5054 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.095463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.053630 restraints weight = 48413.312| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.28 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11000 Z= 0.251 Angle : 0.639 6.593 16944 Z= 0.325 Chirality : 0.036 0.271 2221 Planarity : 0.004 0.018 581 Dihedral : 26.671 178.033 6647 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 4.04 % Allowed : 33.33 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.87), residues: 114 helix: 2.47 (0.76), residues: 48 sheet: -0.71 (1.07), residues: 26 loop : -2.20 (1.08), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 86 TYR 0.008 0.001 TYR B 94 PHE 0.008 0.001 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.25 (11000) covalent geometry : angle 0.63942 / 0.32 (16944) hydrogen bonds : bond 0.08013 / 4.66 ( 369) hydrogen bonds : angle 1.98957 / 1.35 ( 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.134 Fit side-chains REVERT: B 74 GLU cc_start: 0.8691 (mp0) cc_final: 0.8374 (mp0) outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.0904 time to fit residues: 3.2616 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS 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: 40.0000 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.094207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053624 restraints weight = 47901.400| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.39 r_work: 0.2698 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 11000 Z= 0.334 Angle : 0.701 6.482 16944 Z= 0.353 Chirality : 0.039 0.271 2221 Planarity : 0.004 0.018 581 Dihedral : 26.767 178.566 6647 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 4.04 % Allowed : 33.33 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.86), residues: 114 helix: 2.41 (0.76), residues: 48 sheet: -0.98 (1.06), residues: 26 loop : -2.24 (1.07), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 106 TYR 0.008 0.002 TYR B 31 PHE 0.007 0.001 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.33 (11000) covalent geometry : angle 0.70147 / 0.35 (16944) hydrogen bonds : bond 0.09096 / 5.40 ( 369) hydrogen bonds : angle 2.05595 / 1.37 ( 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.143 Fit side-chains REVERT: B 74 GLU cc_start: 0.9018 (mp0) cc_final: 0.8760 (mp0) REVERT: B 91 GLU cc_start: 0.8372 (pm20) cc_final: 0.8140 (pm20) outliers start: 4 outliers final: 4 residues processed: 23 average time/residue: 0.0986 time to fit residues: 3.2977 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 : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.093199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.052095 restraints weight = 48721.527| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.72 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 11000 Z= 0.409 Angle : 0.762 6.920 16944 Z= 0.383 Chirality : 0.042 0.272 2221 Planarity : 0.005 0.019 581 Dihedral : 27.002 178.722 6647 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 5.05 % Allowed : 31.31 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.88), residues: 114 helix: 1.83 (0.76), residues: 54 sheet: -1.26 (1.04), residues: 26 loop : -1.88 (1.22), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 106 TYR 0.009 0.002 TYR B 31 PHE 0.006 0.001 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.41 (11000) covalent geometry : angle 0.76193 / 0.38 (16944) hydrogen bonds : bond 0.09661 / 5.80 ( 369) hydrogen bonds : angle 2.14410 / 1.42 ( 666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3307.39 seconds wall clock time: 57 minutes 14.21 seconds (3434.21 seconds total)