Starting phenix.real_space_refine on Tue Feb 3 12:57:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jke_61552/02_2026/9jke_61552.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jke_61552/02_2026/9jke_61552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jke_61552/02_2026/9jke_61552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jke_61552/02_2026/9jke_61552.map" model { file = "/net/cci-nas-00/data/ceres_data/9jke_61552/02_2026/9jke_61552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jke_61552/02_2026/9jke_61552.cif" } resolution = 3.4 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= 0.002 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: 3 Type Number sf(0) Gaussians C 1662 2.51 5 N 444 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s 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: 2640 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 440 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "B" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 440 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 440 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "D" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 440 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 440 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "F" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 440 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Time building chain proxies: 0.47, per 1000 atoms: 0.18 Number of scatterers: 2640 At special positions: 0 Unit cell: (94.62, 99.6, 35.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 534 8.00 N 444 7.00 C 1662 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: 0.11 Conformation dependent library (CDL) restraints added in 65.6 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 41.7% 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 'C' and resid 38 through 40 removed outlier: 6.620A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 57 removed outlier: 8.394A pdb=" N GLU A 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL C 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASP C 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N HIS A 50 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR C 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 52 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL C 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N GLU C 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA A 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL E 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N HIS E 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP A 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 70 through 71 removed outlier: 7.027A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 78 removed outlier: 6.282A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.376A pdb=" N THR A 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 88 through 96 removed outlier: 6.870A pdb=" N ALA C 91 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY C 93 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA A 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR E 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ALA A 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N PHE E 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY A 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LYS E 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.549A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 46 through 57 removed outlier: 8.324A pdb=" N GLU B 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL D 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N ASP D 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS B 50 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR D 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 52 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N VAL D 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N GLU D 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL F 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS F 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP B 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 70 through 71 removed outlier: 6.987A pdb=" N VAL B 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.306A pdb=" N ALA B 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 81 through 82 removed outlier: 6.374A pdb=" N THR B 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 88 through 96 removed outlier: 6.809A pdb=" N ALA D 91 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B 92 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY D 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA B 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR F 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ALA B 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N PHE F 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LYS F 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) 38 hydrogen bonds defined for protein. 111 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: 0.30 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 462 1.29 - 1.35: 402 1.35 - 1.42: 156 1.42 - 1.48: 444 1.48 - 1.55: 1200 Bond restraints: 2664 Sorted by residual: bond pdb=" CB VAL B 55 " pdb=" CG2 VAL B 55 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.37e+00 bond pdb=" CB VAL D 55 " pdb=" CG2 VAL D 55 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CB VAL C 55 " pdb=" CG2 VAL C 55 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CB VAL F 55 " pdb=" CG2 VAL F 55 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 bond pdb=" CB VAL E 55 " pdb=" CG2 VAL E 55 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 ... (remaining 2659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 3270 1.18 - 2.37: 291 2.37 - 3.55: 57 3.55 - 4.73: 0 4.73 - 5.91: 6 Bond angle restraints: 3624 Sorted by residual: angle pdb=" C VAL F 49 " pdb=" N HIS F 50 " pdb=" CA HIS F 50 " ideal model delta sigma weight residual 122.36 118.91 3.45 1.60e+00 3.91e-01 4.65e+00 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 122.36 118.91 3.45 1.60e+00 3.91e-01 4.64e+00 angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 122.36 118.92 3.44 1.60e+00 3.91e-01 4.62e+00 angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 122.36 118.95 3.41 1.60e+00 3.91e-01 4.55e+00 angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 122.36 118.96 3.40 1.60e+00 3.91e-01 4.53e+00 ... (remaining 3619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.29: 1445 18.29 - 36.58: 49 36.58 - 54.87: 12 54.87 - 73.17: 12 73.17 - 91.46: 12 Dihedral angle restraints: 1530 sinusoidal: 510 harmonic: 1020 Sorted by residual: dihedral pdb=" CA ASP F 98 " pdb=" CB ASP F 98 " pdb=" CG ASP F 98 " pdb=" OD1 ASP F 98 " ideal model delta sinusoidal sigma weight residual -30.00 -88.92 58.92 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP D 98 " pdb=" CB ASP D 98 " pdb=" CG ASP D 98 " pdb=" OD1 ASP D 98 " ideal model delta sinusoidal sigma weight residual -30.00 -88.91 58.91 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP B 98 " pdb=" CB ASP B 98 " pdb=" CG ASP B 98 " pdb=" OD1 ASP B 98 " ideal model delta sinusoidal sigma weight residual -30.00 -88.91 58.91 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 1527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 335 0.052 - 0.104: 77 0.104 - 0.155: 50 0.155 - 0.207: 6 0.207 - 0.258: 6 Chirality restraints: 474 Sorted by residual: chirality pdb=" CB VAL F 55 " pdb=" CA VAL F 55 " pdb=" CG1 VAL F 55 " pdb=" CG2 VAL F 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL B 55 " pdb=" CA VAL B 55 " pdb=" CG1 VAL B 55 " pdb=" CG2 VAL B 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL C 55 " pdb=" CA VAL C 55 " pdb=" CG1 VAL C 55 " pdb=" CG2 VAL C 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 471 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 70 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C VAL C 70 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL C 70 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL C 71 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.011 2.00e-02 2.50e+03 8.96e-03 1.20e+00 pdb=" CG HIS F 50 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " -0.011 2.00e-02 2.50e+03 8.91e-03 1.19e+00 pdb=" CG HIS B 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " -0.004 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1057 2.90 - 3.40: 2401 3.40 - 3.90: 3920 3.90 - 4.40: 4074 4.40 - 4.90: 8740 Nonbonded interactions: 20192 Sorted by model distance: nonbonded pdb=" ND1 HIS D 50 " pdb=" OD1 ASP D 51 " model vdw 2.402 3.120 nonbonded pdb=" ND1 HIS B 50 " pdb=" OD1 ASP B 51 " model vdw 2.402 3.120 nonbonded pdb=" ND1 HIS F 50 " pdb=" OD1 ASP F 51 " model vdw 2.403 3.120 nonbonded pdb=" ND1 HIS C 50 " pdb=" OD1 ASP C 51 " model vdw 2.403 3.120 nonbonded pdb=" ND1 HIS A 50 " pdb=" OD1 ASP A 51 " model vdw 2.403 3.120 ... (remaining 20187 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 0.010 Normalize map: mean=0, sd=1: 2.360 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: 0.010 Set scattering table: 0.000 Process input model: 3.600 Find NCS groups from input model: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.005 0.051 2664 Z= 0.241 Angle : 0.756 5.915 3624 Z= 0.450 Chirality : 0.064 0.258 474 Planarity : 0.003 0.012 444 Dihedral : 16.597 91.456 882 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.36 % Allowed : 4.35 % Favored : 95.29 % 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: -4.99 (0.24), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.18), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR E 39 PHE 0.005 0.001 PHE D 94 TRP 0.003 0.001 TRP F 58 HIS 0.007 0.004 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 2664) covalent geometry : angle 0.75599 ( 3624) hydrogen bonds : bond 0.22476 ( 38) hydrogen bonds : angle 9.94628 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: B 58 TRP cc_start: 0.7645 (m100) cc_final: 0.7433 (m-90) outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.0987 time to fit residues: 6.1896 Evaluate side-chains 43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS D 50 HIS F 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.142402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.120950 restraints weight = 3172.556| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.50 r_work: 0.3769 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2664 Z= 0.121 Angle : 0.483 4.805 3624 Z= 0.272 Chirality : 0.054 0.139 474 Planarity : 0.002 0.009 444 Dihedral : 4.529 32.483 373 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.90 % Allowed : 11.96 % Favored : 85.14 % 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: -4.02 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR E 39 PHE 0.007 0.001 PHE A 94 TRP 0.008 0.001 TRP F 58 HIS 0.004 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 2664) covalent geometry : angle 0.48292 ( 3624) hydrogen bonds : bond 0.02136 ( 38) hydrogen bonds : angle 4.77546 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.063 Fit side-chains revert: symmetry clash REVERT: B 58 TRP cc_start: 0.8162 (m100) cc_final: 0.7888 (m-90) REVERT: E 97 LYS cc_start: 0.8527 (mttt) cc_final: 0.8165 (mttp) outliers start: 8 outliers final: 8 residues processed: 33 average time/residue: 0.0625 time to fit residues: 2.3738 Evaluate side-chains 30 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 0.0670 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.144745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.123217 restraints weight = 2836.857| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.47 r_work: 0.3740 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2664 Z= 0.137 Angle : 0.498 7.794 3624 Z= 0.274 Chirality : 0.053 0.133 474 Planarity : 0.002 0.011 444 Dihedral : 4.356 26.577 373 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.71 % Allowed : 12.68 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.32), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.24), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.009 0.002 PHE A 94 TRP 0.005 0.001 TRP F 58 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 2664) covalent geometry : angle 0.49808 ( 3624) hydrogen bonds : bond 0.02594 ( 38) hydrogen bonds : angle 4.15775 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.092 Fit side-chains REVERT: B 55 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.8090 (t) REVERT: B 58 TRP cc_start: 0.8223 (m100) cc_final: 0.7926 (m-90) REVERT: F 60 LYS cc_start: 0.8680 (tmtt) cc_final: 0.8378 (tptp) outliers start: 13 outliers final: 9 residues processed: 33 average time/residue: 0.0808 time to fit residues: 3.1468 Evaluate side-chains 29 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.139484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.119528 restraints weight = 3148.915| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.32 r_work: 0.3678 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2664 Z= 0.257 Angle : 0.565 7.597 3624 Z= 0.320 Chirality : 0.058 0.149 474 Planarity : 0.002 0.009 444 Dihedral : 5.175 43.500 373 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.99 % Allowed : 14.86 % Favored : 81.16 % 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: -3.11 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR F 39 PHE 0.011 0.002 PHE E 94 TRP 0.004 0.001 TRP D 58 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00590 ( 2664) covalent geometry : angle 0.56499 ( 3624) hydrogen bonds : bond 0.02482 ( 38) hydrogen bonds : angle 4.33093 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.095 Fit side-chains REVERT: B 60 LYS cc_start: 0.8514 (tmtt) cc_final: 0.8205 (tmtt) outliers start: 11 outliers final: 10 residues processed: 37 average time/residue: 0.1167 time to fit residues: 4.8990 Evaluate side-chains 36 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.146056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.126550 restraints weight = 3022.035| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.28 r_work: 0.3784 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2664 Z= 0.087 Angle : 0.444 6.839 3624 Z= 0.247 Chirality : 0.052 0.138 474 Planarity : 0.002 0.007 444 Dihedral : 4.494 43.194 373 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.17 % Allowed : 16.30 % Favored : 81.52 % 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: -2.70 (0.36), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR E 39 PHE 0.006 0.001 PHE A 94 TRP 0.011 0.001 TRP F 58 HIS 0.004 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 2664) covalent geometry : angle 0.44410 ( 3624) hydrogen bonds : bond 0.01776 ( 38) hydrogen bonds : angle 3.65013 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.101 Fit side-chains REVERT: F 60 LYS cc_start: 0.8653 (tmtt) cc_final: 0.8352 (tptp) outliers start: 6 outliers final: 6 residues processed: 29 average time/residue: 0.0981 time to fit residues: 3.2945 Evaluate side-chains 29 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 4 optimal weight: 0.0070 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.150171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.130600 restraints weight = 2935.841| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.33 r_work: 0.3846 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 2664 Z= 0.071 Angle : 0.410 7.045 3624 Z= 0.226 Chirality : 0.052 0.126 474 Planarity : 0.002 0.008 444 Dihedral : 4.094 40.692 373 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.17 % Allowed : 17.75 % Favored : 80.07 % 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: -2.36 (0.38), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR E 39 PHE 0.004 0.001 PHE A 94 TRP 0.010 0.001 TRP F 58 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00148 ( 2664) covalent geometry : angle 0.41017 ( 3624) hydrogen bonds : bond 0.01576 ( 38) hydrogen bonds : angle 3.44960 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.099 Fit side-chains REVERT: D 97 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8126 (mtmt) outliers start: 6 outliers final: 5 residues processed: 22 average time/residue: 0.1108 time to fit residues: 2.8261 Evaluate side-chains 20 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.142357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121196 restraints weight = 2959.986| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.42 r_work: 0.3688 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2664 Z= 0.245 Angle : 0.529 8.295 3624 Z= 0.296 Chirality : 0.056 0.142 474 Planarity : 0.002 0.009 444 Dihedral : 5.069 54.230 373 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.62 % Allowed : 17.03 % Favored : 79.35 % 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: -2.45 (0.38), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR B 39 PHE 0.010 0.002 PHE A 94 TRP 0.011 0.001 TRP F 58 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 2664) covalent geometry : angle 0.52919 ( 3624) hydrogen bonds : bond 0.02014 ( 38) hydrogen bonds : angle 3.80617 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.125 Fit side-chains REVERT: A 54 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8454 (p) REVERT: B 60 LYS cc_start: 0.8449 (tmtt) cc_final: 0.8056 (tmtt) REVERT: F 54 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8062 (m) outliers start: 10 outliers final: 6 residues processed: 35 average time/residue: 0.0886 time to fit residues: 3.5463 Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.142381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121005 restraints weight = 3004.011| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.47 r_work: 0.3688 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2664 Z= 0.229 Angle : 0.531 7.694 3624 Z= 0.299 Chirality : 0.056 0.143 474 Planarity : 0.002 0.008 444 Dihedral : 5.184 54.924 373 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.62 % Allowed : 17.03 % Favored : 79.35 % 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: -2.46 (0.38), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR F 39 PHE 0.010 0.002 PHE A 94 TRP 0.015 0.001 TRP F 58 HIS 0.006 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 2664) covalent geometry : angle 0.53091 ( 3624) hydrogen bonds : bond 0.01880 ( 38) hydrogen bonds : angle 3.76827 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.100 Fit side-chains REVERT: B 60 LYS cc_start: 0.8515 (tmtt) cc_final: 0.8116 (tmtt) REVERT: E 54 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8481 (p) REVERT: F 60 LYS cc_start: 0.8763 (tmtt) cc_final: 0.8488 (tptp) outliers start: 10 outliers final: 8 residues processed: 32 average time/residue: 0.0806 time to fit residues: 2.9790 Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.144550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.124529 restraints weight = 3073.805| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.34 r_work: 0.3760 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2664 Z= 0.118 Angle : 0.456 7.332 3624 Z= 0.253 Chirality : 0.053 0.132 474 Planarity : 0.002 0.006 444 Dihedral : 4.407 41.417 373 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.26 % Allowed : 17.39 % Favored : 79.35 % 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: -2.28 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR F 39 PHE 0.006 0.001 PHE A 94 TRP 0.012 0.001 TRP F 58 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2664) covalent geometry : angle 0.45647 ( 3624) hydrogen bonds : bond 0.01479 ( 38) hydrogen bonds : angle 3.60244 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.096 Fit side-chains REVERT: A 54 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8494 (p) REVERT: D 97 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8185 (mtmt) REVERT: E 54 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8506 (p) REVERT: F 60 LYS cc_start: 0.8691 (tmtt) cc_final: 0.8400 (tptp) outliers start: 9 outliers final: 7 residues processed: 30 average time/residue: 0.0988 time to fit residues: 3.4088 Evaluate side-chains 30 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.144333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.123686 restraints weight = 3057.785| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.42 r_work: 0.3748 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2664 Z= 0.126 Angle : 0.461 7.702 3624 Z= 0.255 Chirality : 0.053 0.133 474 Planarity : 0.002 0.007 444 Dihedral : 4.072 29.585 373 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.35 % Allowed : 16.30 % Favored : 79.35 % 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: -2.17 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR F 39 PHE 0.006 0.001 PHE A 94 TRP 0.012 0.001 TRP F 58 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2664) covalent geometry : angle 0.46068 ( 3624) hydrogen bonds : bond 0.01448 ( 38) hydrogen bonds : angle 3.57304 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.121 Fit side-chains REVERT: A 54 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8444 (p) REVERT: D 97 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8191 (mtmt) REVERT: E 54 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8468 (p) REVERT: F 60 LYS cc_start: 0.8671 (tmtt) cc_final: 0.8386 (tptp) outliers start: 12 outliers final: 9 residues processed: 33 average time/residue: 0.0954 time to fit residues: 3.6639 Evaluate side-chains 32 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.142219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.121148 restraints weight = 2988.237| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.39 r_work: 0.3698 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 2664 Z= 0.288 Angle : 0.565 7.998 3624 Z= 0.320 Chirality : 0.058 0.143 474 Planarity : 0.002 0.009 444 Dihedral : 4.940 41.719 373 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.35 % Allowed : 16.30 % Favored : 79.35 % 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: -2.45 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR B 39 PHE 0.011 0.003 PHE A 94 TRP 0.014 0.001 TRP F 58 HIS 0.007 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00650 ( 2664) covalent geometry : angle 0.56519 ( 3624) hydrogen bonds : bond 0.01900 ( 38) hydrogen bonds : angle 4.01823 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 846.55 seconds wall clock time: 15 minutes 13.98 seconds (913.98 seconds total)