Starting phenix.real_space_refine on Wed Aug 5 13:06:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zii_74275/08_2026/9zii_74275.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zii_74275/08_2026/9zii_74275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zii_74275/08_2026/9zii_74275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zii_74275/08_2026/9zii_74275.map" model { file = "/net/cci-nas-00/data/ceres_data/9zii_74275/08_2026/9zii_74275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zii_74275/08_2026/9zii_74275.cif" } resolution = 3.09 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 31 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9940 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 30, 'rna2p_pyr': 18, 'rna3p_pur': 213, 'rna3p_pyr': 156} Link IDs: {'rna2p': 47, 'rna3p': 369} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Unusual residues: {' MG': 31} Classifications: {'undetermined': 31} Link IDs: {None: 30} Time building chain proxies: 2.87, per 1000 atoms: 0.29 Number of scatterers: 9940 At special positions: 0 Unit cell: (120.048, 178.608, 148.596, 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 31 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: 0.79 Conformation dependent library (CDL) restraints added in 131.2 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 1 sheets defined 47.4% alpha, 17.2% beta 126 base pairs and 205 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'B' and resid 9 through 19 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 removed outlier: 3.561A pdb=" N ALA B 90 " --> pdb=" O GLN B 87 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 6.370A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 320 hydrogen bonds 538 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.18 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: 1063 1.33 - 1.45: 5246 1.45 - 1.57: 3853 1.57 - 1.68: 833 1.68 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 178 " pdb=" C4 A A 178 " ideal model delta sigma weight residual 1.374 1.388 -0.014 6.00e-03 2.78e+04 5.54e+00 bond pdb=" N9 G A 177 " pdb=" C4 G A 177 " ideal model delta sigma weight residual 1.375 1.394 -0.019 8.00e-03 1.56e+04 5.49e+00 bond pdb=" N9 G A 198 " pdb=" C4 G A 198 " ideal model delta sigma weight residual 1.375 1.391 -0.016 8.00e-03 1.56e+04 3.85e+00 bond pdb=" N9 A A 151 " pdb=" C4 A A 151 " ideal model delta sigma weight residual 1.374 1.385 -0.011 6.00e-03 2.78e+04 3.42e+00 bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.364 0.010 6.00e-03 2.78e+04 2.79e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 15388 1.46 - 2.92: 1443 2.92 - 4.38: 93 4.38 - 5.84: 17 5.84 - 7.30: 3 Bond angle restraints: 16944 Sorted by residual: angle pdb=" N3 C A 196 " pdb=" C4 C A 196 " pdb=" N4 C A 196 " ideal model delta sigma weight residual 118.00 112.45 5.55 7.00e-01 2.04e+00 6.29e+01 angle pdb=" O6 G A 198 " pdb=" C6 G A 198 " pdb=" N1 G A 198 " ideal model delta sigma weight residual 119.90 115.20 4.70 6.00e-01 2.78e+00 6.14e+01 angle pdb=" C5 G A 198 " pdb=" C6 G A 198 " pdb=" O6 G A 198 " ideal model delta sigma weight residual 128.60 132.95 -4.35 6.00e-01 2.78e+00 5.24e+01 angle pdb=" N4 C A 196 " pdb=" C4 C A 196 " pdb=" C5 C A 196 " ideal model delta sigma weight residual 120.20 124.91 -4.71 7.00e-01 2.04e+00 4.52e+01 angle pdb=" O2 C A 36 " pdb=" C2 C A 36 " pdb=" N3 C A 36 " ideal model delta sigma weight residual 121.90 117.81 4.09 7.00e-01 2.04e+00 3.42e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.65: 5871 33.65 - 67.30: 1090 67.30 - 100.95: 146 100.95 - 134.60: 3 134.60 - 168.25: 6 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 416 " pdb=" C1' U A 416 " pdb=" N1 U A 416 " pdb=" C2 U A 416 " ideal model delta sinusoidal sigma weight residual 200.00 34.24 165.76 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' U A 67 " pdb=" C1' U A 67 " pdb=" N1 U A 67 " pdb=" C2 U A 67 " ideal model delta sinusoidal sigma weight residual -160.00 -22.41 -137.59 1 1.50e+01 4.44e-03 7.42e+01 dihedral pdb=" O4' U A 199 " pdb=" C1' U A 199 " pdb=" N1 U A 199 " pdb=" C2 U A 199 " ideal model delta sinusoidal sigma weight residual -160.00 -70.40 -89.60 1 1.50e+01 4.44e-03 4.24e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1548 0.041 - 0.082: 222 0.082 - 0.123: 91 0.123 - 0.163: 355 0.163 - 0.204: 5 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C1' A A 50 " pdb=" O4' A A 50 " pdb=" C2' A A 50 " pdb=" N9 A A 50 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1' G A 227 " pdb=" O4' G A 227 " pdb=" C2' G A 227 " pdb=" N9 G A 227 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C3' G A 114 " pdb=" C4' G A 114 " pdb=" O3' G A 114 " pdb=" C2' G A 114 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 196 " -0.015 2.00e-02 2.50e+03 1.75e-02 6.87e+00 pdb=" N1 C A 196 " 0.024 2.00e-02 2.50e+03 pdb=" C2 C A 196 " -0.019 2.00e-02 2.50e+03 pdb=" O2 C A 196 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C A 196 " 0.026 2.00e-02 2.50e+03 pdb=" C4 C A 196 " -0.029 2.00e-02 2.50e+03 pdb=" N4 C A 196 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C A 196 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C A 196 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.033 2.00e-02 2.50e+03 1.41e-02 5.98e+00 pdb=" N9 G A 298 " -0.033 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 187 " -0.029 2.00e-02 2.50e+03 1.40e-02 5.39e+00 pdb=" N9 A A 187 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A A 187 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 187 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 187 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 187 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A A 187 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A A 187 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 187 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A A 187 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 187 " 0.001 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 58 2.58 - 3.16: 7451 3.16 - 3.74: 20837 3.74 - 4.32: 27066 4.32 - 4.90: 34585 Nonbonded interactions: 89997 Sorted by model distance: nonbonded pdb=" O6 G A 299 " pdb="MG MG A 518 " model vdw 1.997 2.170 nonbonded pdb=" OP2 A A 390 " pdb="MG MG A 504 " model vdw 2.009 2.170 nonbonded pdb=" OP2 C A 103 " pdb="MG MG A 509 " model vdw 2.015 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 511 " model vdw 2.020 2.170 nonbonded pdb=" OP1 A A 380 " pdb="MG MG A 526 " model vdw 2.024 2.170 ... (remaining 89992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.890 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 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 0.028 11000 Z= 0.263 Angle : 0.826 7.302 16944 Z= 0.708 Chirality : 0.062 0.204 2221 Planarity : 0.003 0.018 581 Dihedral : 25.756 168.246 6900 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 28.28 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.83), residues: 114 helix: 2.92 (0.74), residues: 47 sheet: 1.21 (0.89), residues: 26 loop : -1.73 (1.08), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.014 0.001 TYR B 5 PHE 0.017 0.002 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.26 (11000) covalent geometry : angle 0.82640 / 0.71 (16944) hydrogen bonds : bond 0.09977 / 10.81 ( 366) hydrogen bonds : angle 2.39505 / 2.68 ( 667) *********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.146 Fit side-chains REVERT: B 35 ARG cc_start: 0.8836 (mmm-85) cc_final: 0.8525 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0986 time to fit residues: 3.2774 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.094466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.052023 restraints weight = 49431.590| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.99 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 11000 Z= 0.461 Angle : 0.835 11.826 16944 Z= 0.435 Chirality : 0.061 0.308 2221 Planarity : 0.006 0.036 581 Dihedral : 25.844 168.803 6645 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.02 % Allowed : 29.29 % 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: 0.69 (0.81), residues: 114 helix: 1.81 (0.69), residues: 48 sheet: 0.87 (0.94), residues: 26 loop : -1.58 (1.13), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.020 0.004 TYR B 31 PHE 0.016 0.003 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.46 (11000) covalent geometry : angle 0.83546 / 0.44 (16944) hydrogen bonds : bond 0.11938 / 12.65 ( 366) hydrogen bonds : angle 2.48533 / 2.93 ( 667) *********************** 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 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.142 Fit side-chains REVERT: B 35 ARG cc_start: 0.9040 (mmm-85) cc_final: 0.8695 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.1128 time to fit residues: 2.8672 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 50.0000 chunk 18 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 overall best weight: 4.8586 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.093975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.051013 restraints weight = 49459.915| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.00 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11000 Z= 0.353 Angle : 0.731 9.137 16944 Z= 0.395 Chirality : 0.051 0.267 2221 Planarity : 0.005 0.022 581 Dihedral : 26.126 168.857 6645 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.02 % Allowed : 31.31 % 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: 0.39 (0.80), residues: 114 helix: 1.66 (0.71), residues: 48 sheet: 0.65 (0.96), residues: 26 loop : -1.82 (1.07), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 26 TYR 0.020 0.003 TYR B 5 PHE 0.013 0.003 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.35 (11000) covalent geometry : angle 0.73072 / 0.40 (16944) hydrogen bonds : bond 0.10832 / 11.40 ( 366) hydrogen bonds : angle 2.35579 / 2.79 ( 667) *********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.140 Fit side-chains REVERT: B 35 ARG cc_start: 0.9051 (mmm-85) cc_final: 0.8748 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.1149 time to fit residues: 3.3945 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 0.1980 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 50.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.093749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.050714 restraints weight = 49024.056| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.01 r_work: 0.2753 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11000 Z= 0.291 Angle : 0.623 8.110 16944 Z= 0.350 Chirality : 0.045 0.262 2221 Planarity : 0.005 0.020 581 Dihedral : 26.073 170.410 6645 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.02 % Allowed : 32.32 % 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: 0.76 (0.83), residues: 114 helix: 2.09 (0.72), residues: 48 sheet: 0.54 (0.96), residues: 26 loop : -1.56 (1.13), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.014 0.003 TYR B 5 PHE 0.012 0.003 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.29 (11000) covalent geometry : angle 0.62297 / 0.35 (16944) hydrogen bonds : bond 0.10512 / 11.39 ( 366) hydrogen bonds : angle 2.23333 / 2.69 ( 667) *********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.149 Fit side-chains REVERT: B 35 ARG cc_start: 0.9032 (mmm-85) cc_final: 0.8765 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 20 average time/residue: 0.0952 time to fit residues: 2.8769 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.091681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048500 restraints weight = 49228.846| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.13 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.093 11000 Z= 0.652 Angle : 1.165 17.682 16944 Z= 0.571 Chirality : 0.078 0.388 2221 Planarity : 0.007 0.030 581 Dihedral : 26.415 170.826 6645 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 33.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 8.08 % Allowed : 29.29 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.78), residues: 114 helix: 0.52 (0.71), residues: 48 sheet: 0.01 (0.93), residues: 26 loop : -1.78 (1.06), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.034 0.005 TYR B 5 PHE 0.017 0.004 PHE B 13 HIS 0.010 0.007 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01050 / 0.65 (11000) covalent geometry : angle 1.16491 / 0.57 (16944) hydrogen bonds : bond 0.15627 / 16.47 ( 366) hydrogen bonds : angle 3.10895 / 3.59 ( 667) *********************** 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: 8 poor density : 18 time to evaluate : 0.147 Fit side-chains REVERT: B 35 ARG cc_start: 0.9179 (mmm-85) cc_final: 0.8877 (mmm-85) outliers start: 8 outliers final: 7 residues processed: 22 average time/residue: 0.1307 time to fit residues: 3.8136 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 50.0000 chunk 17 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.093007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052709 restraints weight = 49221.863| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.15 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11000 Z= 0.317 Angle : 0.694 8.651 16944 Z= 0.383 Chirality : 0.048 0.255 2221 Planarity : 0.005 0.020 581 Dihedral : 26.404 169.257 6645 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 6.06 % Allowed : 29.29 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.81), residues: 114 helix: 1.61 (0.72), residues: 48 sheet: 0.17 (0.94), residues: 26 loop : -1.72 (1.11), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 35 TYR 0.016 0.003 TYR B 5 PHE 0.012 0.003 PHE B 28 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.32 (11000) covalent geometry : angle 0.69357 / 0.38 (16944) hydrogen bonds : bond 0.11312 / 12.11 ( 366) hydrogen bonds : angle 2.41764 / 2.89 ( 667) *********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.146 Fit side-chains REVERT: B 35 ARG cc_start: 0.9085 (mmm-85) cc_final: 0.8823 (mmm-85) outliers start: 6 outliers final: 4 residues processed: 23 average time/residue: 0.1201 time to fit residues: 3.8369 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 67 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 38 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 overall best weight: 5.5386 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.092399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.050680 restraints weight = 49096.876| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.43 r_work: 0.2707 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 11000 Z= 0.439 Angle : 0.799 12.253 16944 Z= 0.423 Chirality : 0.056 0.300 2221 Planarity : 0.005 0.026 581 Dihedral : 26.408 169.482 6645 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 5.05 % Allowed : 31.31 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.81), residues: 114 helix: 1.49 (0.71), residues: 48 sheet: 0.18 (0.96), residues: 26 loop : -1.74 (1.11), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 35 TYR 0.022 0.004 TYR B 5 PHE 0.013 0.003 PHE B 13 HIS 0.005 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.44 (11000) covalent geometry : angle 0.79864 / 0.42 (16944) hydrogen bonds : bond 0.12085 / 12.91 ( 366) hydrogen bonds : angle 2.56120 / 3.06 ( 667) *********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.152 Fit side-chains REVERT: B 35 ARG cc_start: 0.9144 (mmm-85) cc_final: 0.8871 (mmm-85) outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.1547 time to fit residues: 4.2796 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 86 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 50.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.090821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.047542 restraints weight = 49870.062| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.17 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.089 11000 Z= 0.675 Angle : 1.180 17.350 16944 Z= 0.580 Chirality : 0.079 0.386 2221 Planarity : 0.007 0.045 581 Dihedral : 26.651 167.056 6645 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 36.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 8.08 % Allowed : 29.29 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.81), residues: 114 helix: -0.02 (0.70), residues: 54 sheet: -0.28 (0.95), residues: 26 loop : -1.16 (1.26), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.033 0.005 TYR B 5 PHE 0.016 0.004 PHE B 13 HIS 0.010 0.006 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01086 / 0.67 (11000) covalent geometry : angle 1.18040 / 0.58 (16944) hydrogen bonds : bond 0.16133 / 16.91 ( 366) hydrogen bonds : angle 3.14191 / 3.69 ( 667) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.146 Fit side-chains REVERT: B 35 ARG cc_start: 0.9158 (mmm-85) cc_final: 0.8906 (mmm-85) outliers start: 8 outliers final: 6 residues processed: 24 average time/residue: 0.1429 time to fit residues: 4.5890 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 105 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 15 optimal weight: 50.0000 chunk 17 optimal weight: 50.0000 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.092516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051761 restraints weight = 49465.809| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.12 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11000 Z= 0.230 Angle : 0.638 8.394 16944 Z= 0.367 Chirality : 0.044 0.260 2221 Planarity : 0.005 0.022 581 Dihedral : 26.532 170.342 6645 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.02 % Allowed : 34.34 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.83), residues: 114 helix: 1.96 (0.74), residues: 48 sheet: 0.19 (0.96), residues: 26 loop : -1.52 (1.14), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 59 TYR 0.013 0.003 TYR B 5 PHE 0.013 0.002 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.23 (11000) covalent geometry : angle 0.63840 / 0.37 (16944) hydrogen bonds : bond 0.11136 / 12.00 ( 366) hydrogen bonds : angle 2.37615 / 2.91 ( 667) *********************** 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: 2 poor density : 23 time to evaluate : 0.151 Fit side-chains REVERT: B 35 ARG cc_start: 0.8973 (mmm-85) cc_final: 0.8494 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.1013 time to fit residues: 3.5914 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 50.0000 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 overall best weight: 5.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.091881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050448 restraints weight = 49602.293| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.48 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 11000 Z= 0.404 Angle : 0.786 10.989 16944 Z= 0.419 Chirality : 0.055 0.285 2221 Planarity : 0.005 0.021 581 Dihedral : 26.461 170.586 6645 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.03 % Allowed : 31.31 % 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: 0.19 (0.81), residues: 114 helix: 1.42 (0.70), residues: 48 sheet: 0.10 (0.95), residues: 26 loop : -1.44 (1.14), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 86 TYR 0.020 0.003 TYR B 5 PHE 0.013 0.003 PHE B 13 HIS 0.005 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.40 (11000) covalent geometry : angle 0.78647 / 0.42 (16944) hydrogen bonds : bond 0.12076 / 12.91 ( 366) hydrogen bonds : angle 2.53021 / 3.03 ( 667) ********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.133 Fit side-chains REVERT: B 35 ARG cc_start: 0.9136 (mmm-85) cc_final: 0.8868 (mmm-85) outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.0998 time to fit residues: 2.9779 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 67 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 50.0000 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.091516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050687 restraints weight = 49746.543| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.45 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 11000 Z= 0.429 Angle : 0.805 12.304 16944 Z= 0.431 Chirality : 0.056 0.290 2221 Planarity : 0.005 0.022 581 Dihedral : 26.521 169.491 6645 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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: 0.18 (0.84), residues: 114 helix: 0.94 (0.73), residues: 54 sheet: 0.09 (0.96), residues: 26 loop : -1.04 (1.29), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.022 0.003 TYR B 5 PHE 0.016 0.003 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.43 (11000) covalent geometry : angle 0.80519 / 0.43 (16944) hydrogen bonds : bond 0.12386 / 13.25 ( 366) hydrogen bonds : angle 2.60357 / 3.13 ( 667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3754.06 seconds wall clock time: 64 minutes 43.30 seconds (3883.30 seconds total)