Starting phenix.real_space_refine on Tue Aug 4 14:12:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oii_70524/08_2026/9oii_70524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oii_70524/08_2026/9oii_70524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oii_70524/08_2026/9oii_70524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oii_70524/08_2026/9oii_70524.map" model { file = "/net/cci-nas-00/data/ceres_data/9oii_70524/08_2026/9oii_70524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oii_70524/08_2026/9oii_70524.cif" } resolution = 3.2 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= 0.001 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 30 5.16 5 C 2340 2.51 5 N 670 2.21 5 O 670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3710 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 254 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 225 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "C" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 263 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Restraints were copied for chains: D, G, J, M, E, H, K, N, F, I, L, O Time building chain proxies: 0.53, per 1000 atoms: 0.14 Number of scatterers: 3710 At special positions: 0 Unit cell: (106.038, 81.378, 41.1, 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 30 16.00 O 670 8.00 N 670 7.00 C 2340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 22 " distance=2.03 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 22 " distance=2.03 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 22 " distance=2.03 Simple disulfide: pdb=" SG CYS J 5 " - pdb=" SG CYS J 22 " distance=2.03 Simple disulfide: pdb=" SG CYS M 5 " - pdb=" SG CYS M 22 " distance=2.03 Simple disulfide: pdb=" SG CYS E 5 " - pdb=" SG CYS E 22 " distance=2.03 Simple disulfide: pdb=" SG CYS H 5 " - pdb=" SG CYS H 22 " distance=2.03 Simple disulfide: pdb=" SG CYS K 5 " - pdb=" SG CYS K 22 " distance=2.03 Simple disulfide: pdb=" SG CYS N 5 " - pdb=" SG CYS N 22 " distance=2.03 Simple disulfide: pdb=" SG CYS F 5 " - pdb=" SG CYS F 22 " distance=2.03 Simple disulfide: pdb=" SG CYS I 5 " - pdb=" SG CYS I 22 " distance=2.03 Simple disulfide: pdb=" SG CYS L 5 " - pdb=" SG CYS L 22 " distance=2.03 Simple disulfide: pdb=" SG CYS O 5 " - pdb=" SG CYS O 22 " distance=2.03 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: 0.16 Conformation dependent library (CDL) restraints added in 82.9 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 910 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 20 through 21 removed outlier: 6.467A pdb=" N LEU D 20 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 20 " --> pdb=" O ILE D 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 24 through 27 removed outlier: 6.229A pdb=" N THR D 25 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR A 25 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LYS D 28 " --> pdb=" O THR A 25 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS A 27 " --> pdb=" O LYS D 28 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE D 30 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN A 29 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG A 24 " --> pdb=" O THR J 25 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LYS J 27 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 26 " --> pdb=" O LYS J 27 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ASN J 29 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N LYS A 28 " --> pdb=" O ASN J 29 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE J 31 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ILE A 30 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE J 30 " --> pdb=" O ASN M 29 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE M 31 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 5 removed outlier: 6.507A pdb=" N ASN B 4 " --> pdb=" O CYS K 5 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN K 4 " --> pdb=" O CYS N 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 26 through 27 removed outlier: 6.906A pdb=" N VAL E 26 " --> pdb=" O LYS H 27 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 26 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR K 25 " --> pdb=" O VAL N 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 4 through 5 removed outlier: 7.004A pdb=" N ASN C 4 " --> pdb=" O CYS F 5 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN I 4 " --> pdb=" O CYS O 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 11 through 14 removed outlier: 6.672A pdb=" N GLU C 12 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 11 " --> pdb=" O GLU O 12 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS O 14 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASN C 13 " --> pdb=" O LYS O 14 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE I 11 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LYS L 14 " --> pdb=" O PHE I 11 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN I 13 " --> pdb=" O LYS L 14 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 17 through 21 removed outlier: 7.081A pdb=" N GLU C 18 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N LEU O 20 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR C 19 " --> pdb=" O LEU O 20 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR I 19 " --> pdb=" O LEU L 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 26 through 33 removed outlier: 9.043A pdb=" N VAL C 26 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N ASN F 29 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS C 28 " --> pdb=" O ASN F 29 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE F 31 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE C 30 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLU F 33 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU C 32 " --> pdb=" O GLU F 33 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS C 27 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS O 28 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN C 29 " --> pdb=" O LYS O 28 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N VAL I 26 " --> pdb=" O LYS O 27 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N ASN O 29 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS I 28 " --> pdb=" O ASN O 29 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ILE O 31 " --> pdb=" O LYS I 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE I 30 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLU O 33 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU I 32 " --> pdb=" O GLU O 33 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS I 27 " --> pdb=" O VAL L 26 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS L 28 " --> pdb=" O LYS I 27 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN I 29 " --> pdb=" O LYS L 28 " (cutoff:3.500A) 30 hydrogen bonds defined for protein. 90 hydrogen bond angles 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: 0.50 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1220 1.34 - 1.46: 719 1.46 - 1.58: 1786 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 3755 Sorted by residual: bond pdb=" N SER I 3 " pdb=" CA SER I 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N SER O 3 " pdb=" CA SER O 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N SER J 3 " pdb=" CA SER J 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N SER F 3 " pdb=" CA SER F 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 3750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 4160 0.97 - 1.94: 660 1.94 - 2.92: 130 2.92 - 3.89: 55 3.89 - 4.86: 10 Bond angle restraints: 5015 Sorted by residual: angle pdb=" CA PHE E 6 " pdb=" C PHE E 6 " pdb=" O PHE E 6 " ideal model delta sigma weight residual 121.50 118.22 3.28 1.25e+00 6.40e-01 6.87e+00 angle pdb=" CA PHE N 6 " pdb=" C PHE N 6 " pdb=" O PHE N 6 " ideal model delta sigma weight residual 121.50 118.29 3.21 1.25e+00 6.40e-01 6.58e+00 angle pdb=" CA PHE B 6 " pdb=" C PHE B 6 " pdb=" O PHE B 6 " ideal model delta sigma weight residual 121.50 118.30 3.20 1.25e+00 6.40e-01 6.57e+00 angle pdb=" N ALA C 7 " pdb=" CA ALA C 7 " pdb=" C ALA C 7 " ideal model delta sigma weight residual 110.24 113.56 -3.32 1.30e+00 5.92e-01 6.53e+00 angle pdb=" N ALA O 7 " pdb=" CA ALA O 7 " pdb=" C ALA O 7 " ideal model delta sigma weight residual 110.24 113.56 -3.32 1.30e+00 5.92e-01 6.52e+00 ... (remaining 5010 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.66: 1941 14.66 - 29.31: 254 29.31 - 43.97: 125 43.97 - 58.62: 15 58.62 - 73.28: 15 Dihedral angle restraints: 2350 sinusoidal: 1000 harmonic: 1350 Sorted by residual: dihedral pdb=" CA ILE J 30 " pdb=" C ILE J 30 " pdb=" N ILE J 31 " pdb=" CA ILE J 31 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ILE D 30 " pdb=" C ILE D 30 " pdb=" N ILE D 31 " pdb=" CA ILE D 31 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ILE M 30 " pdb=" C ILE M 30 " pdb=" N ILE M 31 " pdb=" CA ILE M 31 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 2347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 229 0.028 - 0.056: 226 0.056 - 0.084: 50 0.084 - 0.112: 11 0.112 - 0.140: 64 Chirality restraints: 580 Sorted by residual: chirality pdb=" CA ILE D 31 " pdb=" N ILE D 31 " pdb=" C ILE D 31 " pdb=" CB ILE D 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE M 31 " pdb=" N ILE M 31 " pdb=" C ILE M 31 " pdb=" CB ILE M 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE J 31 " pdb=" N ILE J 31 " pdb=" C ILE J 31 " pdb=" CB ILE J 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 577 not shown) Planarity restraints: 635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN M 4 " -0.005 2.00e-02 2.50e+03 9.30e-03 8.65e-01 pdb=" CG ASN M 4 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN M 4 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN M 4 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 4 " -0.005 2.00e-02 2.50e+03 9.20e-03 8.46e-01 pdb=" CG ASN D 4 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 4 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 4 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 4 " -0.005 2.00e-02 2.50e+03 9.06e-03 8.22e-01 pdb=" CG ASN J 4 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN J 4 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN J 4 " -0.005 2.00e-02 2.50e+03 ... (remaining 632 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.98: 1712 2.98 - 3.46: 3431 3.46 - 3.94: 5478 3.94 - 4.42: 6292 4.42 - 4.90: 12338 Nonbonded interactions: 29251 Sorted by model distance: nonbonded pdb=" OE1 GLU G 32 " pdb=" NH1 ARG H 9 " model vdw 2.494 3.120 nonbonded pdb=" ND2 ASN C 34 " pdb=" OD1 ASN F 34 " model vdw 2.542 3.120 nonbonded pdb=" NE2 HIS C 10 " pdb=" OE2 GLU O 12 " model vdw 2.548 3.120 nonbonded pdb=" OE1 GLU J 32 " pdb=" NH1 ARG K 9 " model vdw 2.582 3.120 nonbonded pdb=" OE2 GLU I 12 " pdb=" NE2 HIS O 10 " model vdw 2.603 3.120 ... (remaining 29246 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 2.670 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.800 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 0.040 3770 Z= 0.291 Angle : 0.827 4.861 5045 Z= 0.488 Chirality : 0.055 0.140 580 Planarity : 0.003 0.012 635 Dihedral : 16.875 73.278 1395 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.12 % Favored : 85.88 % Rotamer: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % 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: -4.44 (0.29), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.22), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 9 PHE 0.008 0.001 PHE G 11 HIS 0.003 0.001 HIS O 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.29 ( 3755) covalent geometry : angle 0.82732 / 0.49 ( 5015) SS BOND : bond 0.00171 / 0.11 ( 15) SS BOND : angle 0.85388 / 0.56 ( 30) hydrogen bonds : bond 0.23170 / 12.45 ( 30) hydrogen bonds : angle 8.01177 / 5.26 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.160 Fit side-chains REVERT: B 9 ARG cc_start: 0.7719 (tpt90) cc_final: 0.6595 (tpp-160) REVERT: E 9 ARG cc_start: 0.7872 (tpt90) cc_final: 0.6646 (tpp-160) REVERT: F 9 ARG cc_start: 0.8013 (ttt90) cc_final: 0.7335 (tpt90) REVERT: F 24 ARG cc_start: 0.7114 (mtp180) cc_final: 0.6904 (mtm-85) REVERT: G 24 ARG cc_start: 0.6645 (ttm170) cc_final: 0.6301 (ttm110) REVERT: H 9 ARG cc_start: 0.8131 (tpt90) cc_final: 0.7085 (tpp-160) REVERT: K 9 ARG cc_start: 0.7853 (tpt90) cc_final: 0.6607 (tpp-160) REVERT: N 9 ARG cc_start: 0.8126 (tpt90) cc_final: 0.6854 (tpp-160) REVERT: N 24 ARG cc_start: 0.6606 (mtt90) cc_final: 0.6201 (ttm110) REVERT: N 28 LYS cc_start: 0.6612 (mttm) cc_final: 0.5823 (mmmt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1839 time to fit residues: 8.8188 Evaluate side-chains 36 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0030 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.147303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.107379 restraints weight = 3823.399| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.35 r_work: 0.3967 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3770 Z= 0.117 Angle : 0.605 7.811 5045 Z= 0.327 Chirality : 0.052 0.154 580 Planarity : 0.002 0.011 635 Dihedral : 5.854 20.448 475 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 1.90 % Allowed : 14.76 % 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: -3.50 (0.31), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.24), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 24 PHE 0.010 0.001 PHE O 15 HIS 0.002 0.001 HIS C 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 3755) covalent geometry : angle 0.59826 / 0.32 ( 5015) SS BOND : bond 0.00254 / 0.14 ( 15) SS BOND : angle 1.29752 / 0.96 ( 30) hydrogen bonds : bond 0.01373 / 0.89 ( 30) hydrogen bonds : angle 4.31324 / 2.99 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.7865 (tpt90) cc_final: 0.6249 (mmt-90) REVERT: B 20 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7096 (tt) REVERT: E 9 ARG cc_start: 0.8030 (tpt90) cc_final: 0.6428 (mmt-90) REVERT: E 20 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7225 (tt) REVERT: H 9 ARG cc_start: 0.8213 (tpt90) cc_final: 0.7078 (tpp-160) REVERT: H 20 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7330 (tt) REVERT: K 9 ARG cc_start: 0.8068 (tpt90) cc_final: 0.6493 (mmt-90) REVERT: N 9 ARG cc_start: 0.8211 (tpt90) cc_final: 0.7105 (tpp-160) REVERT: N 24 ARG cc_start: 0.6989 (mtt90) cc_final: 0.6540 (ttm110) outliers start: 8 outliers final: 2 residues processed: 43 average time/residue: 0.1453 time to fit residues: 7.1598 Evaluate side-chains 39 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain H residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 = 0.4368 r_free = 0.4368 target = 0.134174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.095241 restraints weight = 3911.176| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 3.32 r_work: 0.3780 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3770 Z= 0.181 Angle : 0.623 9.703 5045 Z= 0.336 Chirality : 0.052 0.143 580 Planarity : 0.002 0.008 635 Dihedral : 5.984 21.410 475 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 1.43 % Allowed : 17.62 % Favored : 80.95 % 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: -2.98 (0.36), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 24 PHE 0.010 0.001 PHE M 11 HIS 0.003 0.001 HIS O 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 3755) covalent geometry : angle 0.61488 / 0.33 ( 5015) SS BOND : bond 0.00104 / 0.06 ( 15) SS BOND : angle 1.40860 / 1.08 ( 30) hydrogen bonds : bond 0.01796 / 1.10 ( 30) hydrogen bonds : angle 4.01593 / 2.88 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.7930 (tpt90) cc_final: 0.6322 (mmt-90) REVERT: B 20 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7201 (tt) REVERT: E 9 ARG cc_start: 0.8116 (tpt90) cc_final: 0.6480 (mmt-90) REVERT: H 9 ARG cc_start: 0.8325 (tpt90) cc_final: 0.7088 (tpp-160) REVERT: K 9 ARG cc_start: 0.8103 (tpt90) cc_final: 0.6513 (mmt-90) REVERT: M 24 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7527 (ttm110) REVERT: N 9 ARG cc_start: 0.8293 (tpt90) cc_final: 0.7167 (tpp-160) REVERT: N 24 ARG cc_start: 0.6895 (mtt90) cc_final: 0.6498 (ttm110) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 0.1722 time to fit residues: 7.2209 Evaluate side-chains 35 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.127542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.089961 restraints weight = 4042.747| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.29 r_work: 0.3663 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 3770 Z= 0.290 Angle : 0.711 10.479 5045 Z= 0.384 Chirality : 0.055 0.155 580 Planarity : 0.003 0.029 635 Dihedral : 6.458 22.880 475 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.06 % Favored : 84.94 % Rotamer: Outliers : 1.67 % Allowed : 17.86 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.35), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 9 PHE 0.016 0.002 PHE G 11 HIS 0.005 0.002 HIS L 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.29 ( 3755) covalent geometry : angle 0.70331 / 0.38 ( 5015) SS BOND : bond 0.00136 / 0.08 ( 15) SS BOND : angle 1.48683 / 1.15 ( 30) hydrogen bonds : bond 0.02118 / 1.33 ( 30) hydrogen bonds : angle 3.85562 / 3.04 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: B 9 ARG cc_start: 0.7984 (tpt90) cc_final: 0.6359 (mmt-90) REVERT: B 20 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7659 (tt) REVERT: E 9 ARG cc_start: 0.8145 (tpt90) cc_final: 0.6443 (mmt-90) REVERT: E 20 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7510 (tt) REVERT: G 24 ARG cc_start: 0.7545 (ttm170) cc_final: 0.7093 (ttm110) REVERT: H 9 ARG cc_start: 0.8432 (tpt90) cc_final: 0.7202 (tpp-160) REVERT: K 9 ARG cc_start: 0.8186 (tpt90) cc_final: 0.6613 (mmt-90) REVERT: M 24 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7543 (ttm110) REVERT: N 9 ARG cc_start: 0.8324 (tpt90) cc_final: 0.6940 (mmt-90) REVERT: N 24 ARG cc_start: 0.6852 (mtt90) cc_final: 0.6495 (ttm110) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 0.1909 time to fit residues: 9.8342 Evaluate side-chains 45 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain H residue 3 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.135136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.096227 restraints weight = 3965.163| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.51 r_work: 0.3796 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3770 Z= 0.139 Angle : 0.592 9.368 5045 Z= 0.321 Chirality : 0.051 0.145 580 Planarity : 0.002 0.026 635 Dihedral : 6.007 22.537 475 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 2.14 % Allowed : 17.86 % Favored : 80.00 % 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: -2.88 (0.37), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 9 PHE 0.009 0.001 PHE C 15 HIS 0.002 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 3755) covalent geometry : angle 0.57800 / 0.32 ( 5015) SS BOND : bond 0.00143 / 0.08 ( 15) SS BOND : angle 1.74765 / 1.39 ( 30) hydrogen bonds : bond 0.01551 / 0.89 ( 30) hydrogen bonds : angle 4.51593 / 3.34 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: B 9 ARG cc_start: 0.7902 (tpt90) cc_final: 0.6255 (mmt-90) REVERT: B 20 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7115 (tt) REVERT: E 9 ARG cc_start: 0.7998 (tpt90) cc_final: 0.6281 (mmt-90) REVERT: G 24 ARG cc_start: 0.7301 (ttm170) cc_final: 0.7074 (ttm110) REVERT: H 9 ARG cc_start: 0.8334 (tpt90) cc_final: 0.6862 (mmt-90) REVERT: K 9 ARG cc_start: 0.8134 (tpt90) cc_final: 0.6522 (mmt-90) REVERT: N 9 ARG cc_start: 0.8283 (tpt90) cc_final: 0.6908 (mmt-90) REVERT: N 24 ARG cc_start: 0.6735 (mtt90) cc_final: 0.6382 (ttm110) outliers start: 9 outliers final: 3 residues processed: 46 average time/residue: 0.1541 time to fit residues: 7.9519 Evaluate side-chains 40 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.125495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.088218 restraints weight = 4276.575| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.43 r_work: 0.3650 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 3770 Z= 0.305 Angle : 0.734 9.978 5045 Z= 0.396 Chirality : 0.054 0.162 580 Planarity : 0.003 0.031 635 Dihedral : 6.693 26.470 475 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % Rotamer: Outliers : 2.62 % Allowed : 16.67 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.36), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 9 PHE 0.016 0.002 PHE D 11 HIS 0.005 0.002 HIS C 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.31 ( 3755) covalent geometry : angle 0.71755 / 0.39 ( 5015) SS BOND : bond 0.00152 / 0.08 ( 15) SS BOND : angle 2.14609 / 1.70 ( 30) hydrogen bonds : bond 0.02211 / 1.35 ( 30) hydrogen bonds : angle 5.23873 / 3.99 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.8003 (tpt90) cc_final: 0.6353 (mmt-90) REVERT: B 20 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7646 (tt) REVERT: E 9 ARG cc_start: 0.8144 (tpt90) cc_final: 0.6485 (mmt-90) REVERT: G 24 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7032 (ttm110) REVERT: H 9 ARG cc_start: 0.8412 (tpt90) cc_final: 0.6940 (mmt-90) REVERT: H 24 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7572 (mtt90) REVERT: K 9 ARG cc_start: 0.8208 (tpt90) cc_final: 0.6688 (mmt-90) REVERT: N 9 ARG cc_start: 0.8337 (tpt90) cc_final: 0.6981 (mmt-90) REVERT: N 24 ARG cc_start: 0.6771 (mtt90) cc_final: 0.6413 (ttm110) REVERT: O 9 ARG cc_start: 0.7236 (ttt90) cc_final: 0.7004 (ttt-90) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 0.1876 time to fit residues: 10.9567 Evaluate side-chains 46 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.135242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.096227 restraints weight = 4083.838| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 3.50 r_work: 0.3789 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3770 Z= 0.147 Angle : 0.618 9.034 5045 Z= 0.334 Chirality : 0.051 0.145 580 Planarity : 0.002 0.028 635 Dihedral : 6.256 25.698 475 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 1.90 % Allowed : 17.62 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.37), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 9 PHE 0.008 0.001 PHE C 15 HIS 0.002 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 3755) covalent geometry : angle 0.60016 / 0.33 ( 5015) SS BOND : bond 0.00154 / 0.09 ( 15) SS BOND : angle 1.99591 / 1.38 ( 30) hydrogen bonds : bond 0.01590 / 0.96 ( 30) hydrogen bonds : angle 4.09808 / 2.96 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.180 Fit side-chains REVERT: B 9 ARG cc_start: 0.7818 (tpt90) cc_final: 0.6196 (mmt-90) REVERT: B 20 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7096 (tt) REVERT: E 9 ARG cc_start: 0.7901 (tpt90) cc_final: 0.6215 (mmt-90) REVERT: H 9 ARG cc_start: 0.8299 (tpt90) cc_final: 0.6854 (mmt-90) REVERT: K 9 ARG cc_start: 0.8182 (tpt90) cc_final: 0.6579 (mmt-90) REVERT: N 9 ARG cc_start: 0.8341 (tpt90) cc_final: 0.6964 (mmt-90) REVERT: N 24 ARG cc_start: 0.6664 (mtt90) cc_final: 0.6329 (ttm110) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.1555 time to fit residues: 8.3064 Evaluate side-chains 40 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.131948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.093449 restraints weight = 4125.312| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.49 r_work: 0.3738 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3770 Z= 0.191 Angle : 0.654 8.948 5045 Z= 0.351 Chirality : 0.052 0.146 580 Planarity : 0.002 0.028 635 Dihedral : 6.433 30.834 475 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.88 % Favored : 86.12 % Rotamer: Outliers : 1.43 % Allowed : 19.29 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.37), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 9 PHE 0.010 0.001 PHE G 11 HIS 0.002 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 ( 3755) covalent geometry : angle 0.64066 / 0.35 ( 5015) SS BOND : bond 0.00115 / 0.06 ( 15) SS BOND : angle 1.80215 / 1.29 ( 30) hydrogen bonds : bond 0.01661 / 1.02 ( 30) hydrogen bonds : angle 4.04361 / 2.99 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: B 9 ARG cc_start: 0.7850 (tpt90) cc_final: 0.6277 (mmt-90) REVERT: B 20 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7513 (tt) REVERT: E 9 ARG cc_start: 0.7959 (tpt90) cc_final: 0.6241 (mmt-90) REVERT: G 24 ARG cc_start: 0.7328 (ttm170) cc_final: 0.7069 (ttm110) REVERT: H 9 ARG cc_start: 0.8301 (tpt90) cc_final: 0.6883 (mmt-90) REVERT: H 24 ARG cc_start: 0.7681 (mtt90) cc_final: 0.7434 (mtt90) REVERT: K 9 ARG cc_start: 0.8172 (tpt90) cc_final: 0.6646 (mmt-90) REVERT: N 9 ARG cc_start: 0.8345 (tpt90) cc_final: 0.6911 (mmt-90) REVERT: N 24 ARG cc_start: 0.6692 (mtt90) cc_final: 0.6313 (ttm110) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.2133 time to fit residues: 10.0210 Evaluate side-chains 43 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.131866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.093434 restraints weight = 4118.933| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 3.47 r_work: 0.3727 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3770 Z= 0.146 Angle : 0.607 8.598 5045 Z= 0.327 Chirality : 0.050 0.143 580 Planarity : 0.003 0.044 635 Dihedral : 6.083 24.732 475 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 1.19 % Allowed : 19.52 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.37), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 9 PHE 0.011 0.001 PHE C 15 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 3755) covalent geometry : angle 0.59556 / 0.32 ( 5015) SS BOND : bond 0.00158 / 0.08 ( 15) SS BOND : angle 1.61441 / 1.18 ( 30) hydrogen bonds : bond 0.01424 / 0.88 ( 30) hydrogen bonds : angle 3.89639 / 2.87 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: B 9 ARG cc_start: 0.7902 (tpt90) cc_final: 0.6298 (mmt-90) REVERT: B 20 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7197 (tt) REVERT: E 9 ARG cc_start: 0.7974 (tpt90) cc_final: 0.6268 (mmt-90) REVERT: H 9 ARG cc_start: 0.8387 (tpt90) cc_final: 0.6980 (mmt-90) REVERT: K 9 ARG cc_start: 0.8209 (tpt90) cc_final: 0.6734 (mmt-90) REVERT: N 9 ARG cc_start: 0.8379 (tpt90) cc_final: 0.6955 (mpt180) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.1621 time to fit residues: 7.1332 Evaluate side-chains 37 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.126279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.088738 restraints weight = 4235.241| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.36 r_work: 0.3660 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3770 Z= 0.221 Angle : 0.699 8.678 5045 Z= 0.373 Chirality : 0.052 0.149 580 Planarity : 0.003 0.041 635 Dihedral : 6.369 26.571 475 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.06 % Favored : 84.94 % Rotamer: Outliers : 1.43 % Allowed : 19.76 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.37), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 9 PHE 0.010 0.001 PHE D 11 HIS 0.003 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 ( 3755) covalent geometry : angle 0.68848 / 0.37 ( 5015) SS BOND : bond 0.00076 / 0.04 ( 15) SS BOND : angle 1.71591 / 1.26 ( 30) hydrogen bonds : bond 0.01691 / 1.04 ( 30) hydrogen bonds : angle 3.95269 / 2.99 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: B 9 ARG cc_start: 0.7971 (tpt90) cc_final: 0.6393 (mmt-90) REVERT: B 20 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7690 (tt) REVERT: E 9 ARG cc_start: 0.8052 (tpt90) cc_final: 0.6370 (mmt-90) REVERT: E 24 ARG cc_start: 0.6812 (mtt90) cc_final: 0.6305 (ttm110) REVERT: F 14 LYS cc_start: 0.8453 (mttp) cc_final: 0.8114 (mptt) REVERT: G 24 ARG cc_start: 0.7488 (ttm170) cc_final: 0.7240 (ttm110) REVERT: H 9 ARG cc_start: 0.8384 (tpt90) cc_final: 0.7006 (mmt-90) REVERT: H 24 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7492 (mtt90) REVERT: K 9 ARG cc_start: 0.8226 (tpt90) cc_final: 0.6720 (mmt-90) REVERT: N 9 ARG cc_start: 0.8417 (tpt90) cc_final: 0.7019 (mmt-90) REVERT: N 24 ARG cc_start: 0.6825 (mtt90) cc_final: 0.6439 (ttm110) REVERT: O 9 ARG cc_start: 0.7195 (ttt90) cc_final: 0.6796 (tmt170) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.1709 time to fit residues: 8.2147 Evaluate side-chains 42 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.128549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.090703 restraints weight = 4107.079| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.39 r_work: 0.3683 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3770 Z= 0.183 Angle : 0.679 8.634 5045 Z= 0.363 Chirality : 0.051 0.147 580 Planarity : 0.003 0.040 635 Dihedral : 6.267 26.081 475 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 1.19 % Allowed : 20.71 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.37), residues: 425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 9 PHE 0.009 0.001 PHE G 11 HIS 0.002 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 ( 3755) covalent geometry : angle 0.66945 / 0.36 ( 5015) SS BOND : bond 0.00117 / 0.06 ( 15) SS BOND : angle 1.58865 / 1.18 ( 30) hydrogen bonds : bond 0.01630 / 1.02 ( 30) hydrogen bonds : angle 3.92727 / 2.97 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1175.84 seconds wall clock time: 20 minutes 53.57 seconds (1253.57 seconds total)