Starting phenix.real_space_refine on Tue Feb 3 12:19:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ktz_62571/02_2026/9ktz_62571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ktz_62571/02_2026/9ktz_62571.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/9ktz_62571/02_2026/9ktz_62571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ktz_62571/02_2026/9ktz_62571.map" model { file = "/net/cci-nas-00/data/ceres_data/9ktz_62571/02_2026/9ktz_62571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ktz_62571/02_2026/9ktz_62571.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= 0.000 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 486 2.51 5 N 144 2.21 5 O 156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 792 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 132 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Restraints were copied for chains: E, A, D, C, F Time building chain proxies: 0.13, per 1000 atoms: 0.16 Number of scatterers: 792 At special positions: 0 Unit cell: (51, 66, 30, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 156 8.00 N 144 7.00 C 486 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: 0.04 Conformation dependent library (CDL) restraints added in 21.6 milliseconds 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 270 1.34 - 1.45: 184 1.45 - 1.57: 344 1.57 - 1.68: 0 1.68 - 1.80: 12 Bond restraints: 810 Sorted by residual: bond pdb=" C GLN E 22 " pdb=" N THR E 23 " ideal model delta sigma weight residual 1.330 1.320 0.009 1.37e-02 5.33e+03 4.70e-01 bond pdb=" C GLN C 22 " pdb=" N THR C 23 " ideal model delta sigma weight residual 1.330 1.320 0.009 1.37e-02 5.33e+03 4.44e-01 bond pdb=" C GLN D 22 " pdb=" N THR D 23 " ideal model delta sigma weight residual 1.330 1.321 0.009 1.37e-02 5.33e+03 4.35e-01 bond pdb=" C GLN F 22 " pdb=" N THR F 23 " ideal model delta sigma weight residual 1.330 1.321 0.009 1.37e-02 5.33e+03 4.33e-01 bond pdb=" C GLN A 22 " pdb=" N THR A 23 " ideal model delta sigma weight residual 1.330 1.321 0.009 1.37e-02 5.33e+03 4.03e-01 ... (remaining 805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 929 1.11 - 2.23: 115 2.23 - 3.34: 24 3.34 - 4.46: 6 4.46 - 5.57: 12 Bond angle restraints: 1086 Sorted by residual: angle pdb=" C ALA C 14 " pdb=" N TRP C 15 " pdb=" CA TRP C 15 " ideal model delta sigma weight residual 122.03 116.46 5.57 2.01e+00 2.48e-01 7.68e+00 angle pdb=" C ALA E 14 " pdb=" N TRP E 15 " pdb=" CA TRP E 15 " ideal model delta sigma weight residual 122.03 116.48 5.55 2.01e+00 2.48e-01 7.63e+00 angle pdb=" C ALA F 14 " pdb=" N TRP F 15 " pdb=" CA TRP F 15 " ideal model delta sigma weight residual 122.03 116.48 5.55 2.01e+00 2.48e-01 7.62e+00 angle pdb=" C ALA A 14 " pdb=" N TRP A 15 " pdb=" CA TRP A 15 " ideal model delta sigma weight residual 122.03 116.49 5.54 2.01e+00 2.48e-01 7.60e+00 angle pdb=" C ALA D 14 " pdb=" N TRP D 15 " pdb=" CA TRP D 15 " ideal model delta sigma weight residual 122.03 116.51 5.52 2.01e+00 2.48e-01 7.54e+00 ... (remaining 1081 not shown) Histogram of dihedral angle deviations from ideal: 0.05 - 16.70: 384 16.70 - 33.36: 30 33.36 - 50.02: 12 50.02 - 66.67: 6 66.67 - 83.33: 12 Dihedral angle restraints: 444 sinusoidal: 180 harmonic: 264 Sorted by residual: dihedral pdb=" CA PHE F 20 " pdb=" C PHE F 20 " pdb=" N ASN F 21 " pdb=" CA ASN F 21 " ideal model delta harmonic sigma weight residual -180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE A 20 " pdb=" C PHE A 20 " pdb=" N ASN A 21 " pdb=" CA ASN A 21 " ideal model delta harmonic sigma weight residual -180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE B 20 " pdb=" C PHE B 20 " pdb=" N ASN B 21 " pdb=" CA ASN B 21 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.019: 26 0.019 - 0.038: 8 0.038 - 0.056: 34 0.056 - 0.075: 10 0.075 - 0.094: 12 Chirality restraints: 90 Sorted by residual: chirality pdb=" CA TRP D 15 " pdb=" N TRP D 15 " pdb=" C TRP D 15 " pdb=" CB TRP D 15 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.21e-01 chirality pdb=" CA TRP A 15 " pdb=" N TRP A 15 " pdb=" C TRP A 15 " pdb=" CB TRP A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.07e-01 chirality pdb=" CA TRP F 15 " pdb=" N TRP F 15 " pdb=" C TRP F 15 " pdb=" CB TRP F 15 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.05e-01 ... (remaining 87 not shown) Planarity restraints: 150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 15 " 0.043 2.00e-02 2.50e+03 3.32e-02 2.76e+01 pdb=" CG TRP C 15 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP C 15 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP C 15 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP C 15 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 15 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 15 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 15 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 15 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 15 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 15 " -0.043 2.00e-02 2.50e+03 3.32e-02 2.76e+01 pdb=" CG TRP E 15 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP E 15 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP E 15 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP E 15 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 15 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 15 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 15 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 15 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 15 " -0.043 2.00e-02 2.50e+03 3.32e-02 2.75e+01 pdb=" CG TRP F 15 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP F 15 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP F 15 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 15 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 15 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 15 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 15 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 15 " -0.008 2.00e-02 2.50e+03 ... (remaining 147 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 41 2.72 - 3.26: 806 3.26 - 3.81: 1251 3.81 - 4.35: 1587 4.35 - 4.90: 2554 Nonbonded interactions: 6239 Sorted by model distance: nonbonded pdb=" O THR B 23 " pdb=" NE2 GLN E 13 " model vdw 2.175 3.120 nonbonded pdb=" O THR C 23 " pdb=" NE2 GLN F 13 " model vdw 2.235 3.120 nonbonded pdb=" O THR A 23 " pdb=" NE2 GLN D 13 " model vdw 2.339 3.120 nonbonded pdb=" O THR E 23 " pdb=" NE2 GLN A 13 " model vdw 2.359 3.120 nonbonded pdb=" NE1 TRP D 15 " pdb=" OE1 GLN D 17 " model vdw 2.361 3.120 ... (remaining 6234 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'A' selection = chain 'D' selection = chain 'C' selection = chain 'F' } 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: 6.480 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.220 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 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 : 0.006 0.019 810 Z= 0.292 Angle : 0.929 5.570 1086 Z= 0.533 Chirality : 0.048 0.094 90 Planarity : 0.008 0.033 150 Dihedral : 22.532 83.331 276 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -5.46 (0.58), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.44), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.008 TYR E 11 PHE 0.008 0.004 PHE C 20 TRP 0.088 0.019 TRP C 15 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 810) covalent geometry : angle 0.92918 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0227 time to fit residues: 0.5259 Evaluate side-chains 19 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 overall best weight: 0.4313 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN D 18 GLN C 18 GLN F 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.141959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.128834 restraints weight = 1121.090| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.90 r_work: 0.4014 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 810 Z= 0.167 Angle : 0.733 4.676 1086 Z= 0.405 Chirality : 0.042 0.073 90 Planarity : 0.004 0.019 150 Dihedral : 6.714 15.737 96 Min Nonbonded Distance : 2.676 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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: -5.57 (0.54), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.41), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR C 11 PHE 0.009 0.003 PHE E 20 TRP 0.051 0.011 TRP E 15 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 810) covalent geometry : angle 0.73258 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0214 time to fit residues: 0.4991 Evaluate side-chains 19 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5647 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.137643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.123212 restraints weight = 1003.420| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.70 r_work: 0.3928 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 810 Z= 0.202 Angle : 0.794 5.788 1086 Z= 0.437 Chirality : 0.043 0.081 90 Planarity : 0.004 0.017 150 Dihedral : 6.895 17.074 96 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 21.79 % Favored : 78.21 % 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: -5.33 (0.56), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.43), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR C 11 PHE 0.010 0.004 PHE D 20 TRP 0.045 0.010 TRP E 15 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 810) covalent geometry : angle 0.79421 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0476 time to fit residues: 1.0259 Evaluate side-chains 19 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.132981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.118252 restraints weight = 968.571| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.69 r_work: 0.3912 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 810 Z= 0.184 Angle : 0.758 6.043 1086 Z= 0.414 Chirality : 0.043 0.081 90 Planarity : 0.003 0.014 150 Dihedral : 6.509 15.518 96 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.85 % Allowed : 24.36 % Favored : 71.79 % 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: -5.22 (0.56), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.43), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR C 11 PHE 0.010 0.004 PHE E 20 TRP 0.037 0.008 TRP E 15 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 810) covalent geometry : angle 0.75831 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.032 Fit side-chains revert: symmetry clash REVERT: B 15 TRP cc_start: 0.8020 (OUTLIER) cc_final: 0.7383 (p90) REVERT: E 15 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.7572 (p90) outliers start: 3 outliers final: 1 residues processed: 21 average time/residue: 0.0363 time to fit residues: 0.9171 Evaluate side-chains 22 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain D residue 18 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 overall best weight: 0.3610 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.142031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.127173 restraints weight = 1001.605| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.70 r_work: 0.3950 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 810 Z= 0.147 Angle : 0.704 5.683 1086 Z= 0.382 Chirality : 0.041 0.072 90 Planarity : 0.003 0.013 150 Dihedral : 6.053 14.271 96 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.56 % Allowed : 28.21 % Favored : 69.23 % 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: -5.22 (0.55), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.42), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 11 PHE 0.010 0.003 PHE E 20 TRP 0.034 0.006 TRP B 15 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 810) covalent geometry : angle 0.70375 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.031 Fit side-chains REVERT: B 15 TRP cc_start: 0.7949 (OUTLIER) cc_final: 0.7402 (p90) REVERT: E 15 TRP cc_start: 0.7994 (OUTLIER) cc_final: 0.7570 (p90) REVERT: A 11 TYR cc_start: 0.8263 (m-10) cc_final: 0.7979 (m-10) outliers start: 2 outliers final: 0 residues processed: 20 average time/residue: 0.0346 time to fit residues: 0.8031 Evaluate side-chains 20 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain E residue 15 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 overall best weight: 0.4647 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.132472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.117524 restraints weight = 979.589| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.66 r_work: 0.3903 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 810 Z= 0.175 Angle : 0.740 6.060 1086 Z= 0.403 Chirality : 0.042 0.080 90 Planarity : 0.003 0.015 150 Dihedral : 6.282 15.302 96 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 7.69 % Allowed : 24.36 % Favored : 67.95 % 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: -5.08 (0.56), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.42), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 11 PHE 0.010 0.004 PHE B 20 TRP 0.038 0.007 TRP B 15 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 810) covalent geometry : angle 0.73961 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.030 Fit side-chains revert: symmetry clash REVERT: B 15 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.7274 (p90) REVERT: E 15 TRP cc_start: 0.8086 (OUTLIER) cc_final: 0.7711 (p90) REVERT: A 11 TYR cc_start: 0.8158 (m-10) cc_final: 0.7889 (m-10) REVERT: C 15 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.7587 (p90) REVERT: F 18 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7672 (mp-120) outliers start: 6 outliers final: 1 residues processed: 22 average time/residue: 0.0336 time to fit residues: 0.8595 Evaluate side-chains 23 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain C residue 15 TRP Chi-restraints excluded: chain F residue 18 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 overall best weight: 0.4647 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.135861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.121421 restraints weight = 978.168| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.58 r_work: 0.3920 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 810 Z= 0.176 Angle : 0.747 6.064 1086 Z= 0.407 Chirality : 0.043 0.080 90 Planarity : 0.003 0.015 150 Dihedral : 6.262 15.140 96 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 8.97 % Allowed : 23.08 % Favored : 67.95 % 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: -5.01 (0.56), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.43), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 11 PHE 0.010 0.004 PHE E 20 TRP 0.039 0.007 TRP E 15 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 810) covalent geometry : angle 0.74702 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.032 Fit side-chains revert: symmetry clash REVERT: B 15 TRP cc_start: 0.8076 (OUTLIER) cc_final: 0.7001 (p90) REVERT: E 15 TRP cc_start: 0.8115 (OUTLIER) cc_final: 0.7805 (p90) REVERT: A 15 TRP cc_start: 0.7917 (OUTLIER) cc_final: 0.6553 (p90) REVERT: C 15 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.7618 (p90) REVERT: F 18 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7672 (mp-120) outliers start: 7 outliers final: 2 residues processed: 23 average time/residue: 0.0342 time to fit residues: 0.9130 Evaluate side-chains 25 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain C residue 15 TRP Chi-restraints excluded: chain F residue 18 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 4 optimal weight: 0.0060 chunk 5 optimal weight: 0.8980 overall best weight: 0.2673 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.142888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.129096 restraints weight = 961.822| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.52 r_work: 0.4033 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 810 Z= 0.128 Angle : 0.664 5.446 1086 Z= 0.359 Chirality : 0.041 0.075 90 Planarity : 0.002 0.012 150 Dihedral : 5.554 12.829 96 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 6.41 % Allowed : 25.64 % Favored : 67.95 % 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: -5.07 (0.55), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.42), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR C 11 PHE 0.010 0.003 PHE D 20 TRP 0.032 0.005 TRP E 15 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 810) covalent geometry : angle 0.66399 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.034 Fit side-chains REVERT: B 15 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.7624 (p90) REVERT: E 15 TRP cc_start: 0.8087 (OUTLIER) cc_final: 0.7688 (p90) REVERT: D 18 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7021 (mp-120) REVERT: F 18 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7560 (mp-120) outliers start: 5 outliers final: 1 residues processed: 21 average time/residue: 0.0309 time to fit residues: 0.7649 Evaluate side-chains 23 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 TRP Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain F residue 18 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 0.0970 chunk 4 optimal weight: 0.0570 chunk 5 optimal weight: 0.2980 overall best weight: 0.1507 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.152590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.139024 restraints weight = 932.562| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.59 r_work: 0.4130 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 810 Z= 0.109 Angle : 0.607 4.860 1086 Z= 0.329 Chirality : 0.040 0.081 90 Planarity : 0.002 0.010 150 Dihedral : 4.904 10.990 96 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.56 % Allowed : 29.49 % Favored : 67.95 % 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: -5.13 (0.52), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.40), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 11 PHE 0.008 0.002 PHE D 20 TRP 0.026 0.003 TRP E 15 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 810) covalent geometry : angle 0.60749 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.030 Fit side-chains REVERT: D 18 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7218 (mp-120) outliers start: 2 outliers final: 1 residues processed: 19 average time/residue: 0.0325 time to fit residues: 0.7236 Evaluate side-chains 20 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain D residue 18 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4647 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.137675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.123545 restraints weight = 978.683| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.56 r_work: 0.3942 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 810 Z= 0.172 Angle : 0.720 5.923 1086 Z= 0.393 Chirality : 0.041 0.076 90 Planarity : 0.003 0.015 150 Dihedral : 5.990 15.120 96 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.85 % Allowed : 29.49 % 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: -5.06 (0.54), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.41), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 11 PHE 0.009 0.003 PHE D 20 TRP 0.039 0.007 TRP B 15 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 810) covalent geometry : angle 0.72033 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.018 Fit side-chains revert: symmetry clash REVERT: F 18 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7469 (mp-120) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 0.0204 time to fit residues: 0.4596 Evaluate side-chains 21 residues out of total 78 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain F residue 18 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 0.0470 chunk 5 optimal weight: 0.0060 overall best weight: 0.1503 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.148665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.135140 restraints weight = 962.473| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.61 r_work: 0.4095 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 810 Z= 0.111 Angle : 0.609 4.854 1086 Z= 0.330 Chirality : 0.040 0.080 90 Planarity : 0.002 0.009 150 Dihedral : 4.984 11.411 96 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.13 % Allowed : 28.21 % 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: -5.13 (0.52), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.39), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 11 PHE 0.009 0.002 PHE D 20 TRP 0.024 0.003 TRP B 15 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 810) covalent geometry : angle 0.60923 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 539.08 seconds wall clock time: 10 minutes 3.87 seconds (603.87 seconds total)