Starting phenix.real_space_refine on Tue Feb 3 15:12:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qyn_53456/02_2026/9qyn_53456.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qyn_53456/02_2026/9qyn_53456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qyn_53456/02_2026/9qyn_53456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qyn_53456/02_2026/9qyn_53456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qyn_53456/02_2026/9qyn_53456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qyn_53456/02_2026/9qyn_53456.map" } resolution = 3.13 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= 0.004 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 2610 2.51 5 N 720 2.21 5 O 830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4160 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 416 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "H" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 416 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "I" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 416 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "J" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 416 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "K" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 416 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "L" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 416 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "M" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 416 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "N" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 416 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "O" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 416 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "P" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 416 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Time building chain proxies: 1.14, per 1000 atoms: 0.27 Number of scatterers: 4160 At special positions: 0 Unit cell: (94.9, 94.9, 41.6, 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 830 8.00 N 720 7.00 C 2610 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: 0.33 Conformation dependent library (CDL) restraints added in 184.7 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 60.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 37 through 40 removed outlier: 6.276A pdb=" N VAL G 37 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL I 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL I 37 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL K 40 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR I 39 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL K 37 " --> pdb=" O LEU M 38 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL M 40 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR K 39 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL M 37 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL O 40 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR M 39 " --> pdb=" O VAL O 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 43 through 49 removed outlier: 6.837A pdb=" N VAL G 48 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL I 49 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL I 48 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL K 49 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL K 48 " --> pdb=" O GLY M 47 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL M 49 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL M 48 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL O 49 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 52 through 58 removed outlier: 6.174A pdb=" N VAL M 52 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL O 55 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR M 54 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLU O 57 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA M 56 " --> pdb=" O GLU O 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 61 through 66 removed outlier: 6.648A pdb=" N GLU G 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N THR I 64 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL G 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL I 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASN G 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU I 61 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR K 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL I 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL K 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN I 65 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU K 61 " --> pdb=" O GLN M 62 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N THR M 64 " --> pdb=" O GLU K 61 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL K 63 " --> pdb=" O THR M 64 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL M 66 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN K 65 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU M 61 " --> pdb=" O GLN O 62 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR O 64 " --> pdb=" O GLU M 61 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL M 63 " --> pdb=" O THR O 64 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL O 66 " --> pdb=" O VAL M 63 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN M 65 " --> pdb=" O VAL O 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 69 through 72 Processing sheet with id=AA6, first strand: chain 'G' and resid 75 through 82 removed outlier: 6.861A pdb=" N ALA G 76 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA I 76 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA K 76 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA M 76 " --> pdb=" O THR O 75 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 86 through 88 removed outlier: 6.493A pdb=" N SER G 87 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER M 87 " --> pdb=" O ILE O 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 37 through 40 removed outlier: 6.394A pdb=" N VAL H 37 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL J 40 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR H 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL J 37 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL L 40 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR J 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL L 37 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL N 40 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR L 39 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL N 37 " --> pdb=" O LEU P 38 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL P 40 " --> pdb=" O VAL N 37 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR N 39 " --> pdb=" O VAL P 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 43 through 49 removed outlier: 6.891A pdb=" N VAL H 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL J 49 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL J 48 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL L 49 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL L 48 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL N 49 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 43 through 49 removed outlier: 6.891A pdb=" N VAL H 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL J 49 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL J 48 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL L 49 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL L 48 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL N 49 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL N 48 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL P 49 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS N 50 " --> pdb=" O VAL P 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 61 through 66 removed outlier: 6.590A pdb=" N GLU H 61 " --> pdb=" O GLN J 62 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR J 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL H 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL J 66 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN H 65 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU J 61 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR L 64 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL J 63 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL L 66 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN J 65 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU L 61 " --> pdb=" O GLN N 62 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR N 64 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL L 63 " --> pdb=" O THR N 64 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL N 66 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN L 65 " --> pdb=" O VAL N 66 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU N 61 " --> pdb=" O GLN P 62 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR P 64 " --> pdb=" O GLU N 61 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL N 63 " --> pdb=" O THR P 64 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL P 66 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN N 65 " --> pdb=" O VAL P 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 69 through 72 Processing sheet with id=AB5, first strand: chain 'H' and resid 75 through 82 removed outlier: 6.870A pdb=" N ALA H 76 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA J 76 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA L 76 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA N 76 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 86 through 88 removed outlier: 6.603A pdb=" N SER H 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER J 87 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER L 87 " --> pdb=" O ILE N 88 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER N 87 " --> pdb=" O ILE P 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'H' and resid 91 through 92 173 hydrogen bonds defined for protein. 516 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: 0.62 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.30: 720 1.30 - 1.38: 770 1.38 - 1.46: 702 1.46 - 1.54: 1931 1.54 - 1.62: 57 Bond restraints: 4180 Sorted by residual: bond pdb=" CA HIS M 50 " pdb=" CB HIS M 50 " ideal model delta sigma weight residual 1.539 1.619 -0.080 4.88e-02 4.20e+02 2.66e+00 bond pdb=" CA HIS O 50 " pdb=" CB HIS O 50 " ideal model delta sigma weight residual 1.539 1.616 -0.076 4.88e-02 4.20e+02 2.44e+00 bond pdb=" CA HIS K 50 " pdb=" CB HIS K 50 " ideal model delta sigma weight residual 1.539 1.616 -0.076 4.88e-02 4.20e+02 2.44e+00 bond pdb=" CA HIS I 50 " pdb=" CB HIS I 50 " ideal model delta sigma weight residual 1.539 1.613 -0.073 4.88e-02 4.20e+02 2.26e+00 bond pdb=" CB VAL H 48 " pdb=" CG1 VAL H 48 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.23e+00 ... (remaining 4175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 5482 1.48 - 2.95: 150 2.95 - 4.43: 20 4.43 - 5.90: 3 5.90 - 7.38: 5 Bond angle restraints: 5660 Sorted by residual: angle pdb=" N HIS J 50 " pdb=" CA HIS J 50 " pdb=" CB HIS J 50 " ideal model delta sigma weight residual 110.56 116.65 -6.09 1.86e+00 2.89e-01 1.07e+01 angle pdb=" N HIS I 50 " pdb=" CA HIS I 50 " pdb=" CB HIS I 50 " ideal model delta sigma weight residual 110.32 117.70 -7.38 2.44e+00 1.68e-01 9.15e+00 angle pdb=" N HIS M 50 " pdb=" CA HIS M 50 " pdb=" CB HIS M 50 " ideal model delta sigma weight residual 110.32 117.46 -7.14 2.44e+00 1.68e-01 8.55e+00 angle pdb=" N HIS O 50 " pdb=" CA HIS O 50 " pdb=" CB HIS O 50 " ideal model delta sigma weight residual 110.32 117.34 -7.02 2.44e+00 1.68e-01 8.27e+00 angle pdb=" N HIS K 50 " pdb=" CA HIS K 50 " pdb=" CB HIS K 50 " ideal model delta sigma weight residual 110.32 117.26 -6.94 2.44e+00 1.68e-01 8.09e+00 ... (remaining 5655 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.84: 2261 11.84 - 23.67: 93 23.67 - 35.50: 17 35.50 - 47.33: 18 47.33 - 59.16: 21 Dihedral angle restraints: 2410 sinusoidal: 780 harmonic: 1630 Sorted by residual: dihedral pdb=" CA GLN O 79 " pdb=" C GLN O 79 " pdb=" N LYS O 80 " pdb=" CA LYS O 80 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA GLN P 79 " pdb=" C GLN P 79 " pdb=" N LYS P 80 " pdb=" CA LYS P 80 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA GLN I 79 " pdb=" C GLN I 79 " pdb=" N LYS I 80 " pdb=" CA LYS I 80 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 2407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 396 0.027 - 0.053: 160 0.053 - 0.080: 52 0.080 - 0.107: 70 0.107 - 0.133: 72 Chirality restraints: 750 Sorted by residual: chirality pdb=" CA VAL I 48 " pdb=" N VAL I 48 " pdb=" C VAL I 48 " pdb=" CB VAL I 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL L 55 " pdb=" N VAL L 55 " pdb=" C VAL L 55 " pdb=" CB VAL L 55 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA VAL O 48 " pdb=" N VAL O 48 " pdb=" C VAL O 48 " pdb=" CB VAL O 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 747 not shown) Planarity restraints: 700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 39 " 0.013 2.00e-02 2.50e+03 1.03e-02 2.14e+00 pdb=" CG TYR O 39 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR O 39 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR O 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR O 39 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR O 39 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR O 39 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR O 39 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 59 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C THR J 59 " -0.025 2.00e-02 2.50e+03 pdb=" O THR J 59 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS J 60 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 39 " 0.012 2.00e-02 2.50e+03 9.98e-03 1.99e+00 pdb=" CG TYR I 39 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR I 39 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR I 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR I 39 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR I 39 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR I 39 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR I 39 " -0.003 2.00e-02 2.50e+03 ... (remaining 697 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1530 2.89 - 3.39: 3382 3.39 - 3.90: 6574 3.90 - 4.40: 7080 4.40 - 4.90: 15153 Nonbonded interactions: 33719 Sorted by model distance: nonbonded pdb=" O SER K 42 " pdb=" OG SER M 42 " model vdw 2.392 3.040 nonbonded pdb=" O SER G 42 " pdb=" OG SER I 42 " model vdw 2.415 3.040 nonbonded pdb=" O SER H 42 " pdb=" OG SER J 42 " model vdw 2.416 3.040 nonbonded pdb=" O SER J 42 " pdb=" OG SER L 42 " model vdw 2.418 3.040 nonbonded pdb=" O SER I 42 " pdb=" OG SER K 42 " model vdw 2.420 3.040 ... (remaining 33714 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 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 1.220 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.300 Find NCS groups from input model: 0.080 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.004 0.080 4180 Z= 0.137 Angle : 0.637 7.379 5660 Z= 0.371 Chirality : 0.054 0.133 750 Planarity : 0.002 0.014 700 Dihedral : 10.978 59.156 1390 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.67 % Allowed : 1.90 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.29), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.007 TYR I 39 PHE 0.009 0.002 PHE O 94 HIS 0.009 0.004 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4180) covalent geometry : angle 0.63691 ( 5660) hydrogen bonds : bond 0.13318 ( 161) hydrogen bonds : angle 6.85419 ( 516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.151 Fit side-chains REVERT: G 45 LYS cc_start: 0.8883 (mttt) cc_final: 0.8512 (mttm) REVERT: G 60 LYS cc_start: 0.8579 (tttt) cc_final: 0.8193 (tttt) REVERT: G 83 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7617 (tm-30) REVERT: H 45 LYS cc_start: 0.8882 (mttt) cc_final: 0.8594 (mttm) REVERT: H 60 LYS cc_start: 0.8593 (tttt) cc_final: 0.8391 (tttt) REVERT: H 83 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7599 (tm-30) REVERT: I 45 LYS cc_start: 0.8655 (mttt) cc_final: 0.8397 (mttm) REVERT: I 60 LYS cc_start: 0.8341 (tttt) cc_final: 0.8037 (tttp) REVERT: M 45 LYS cc_start: 0.8534 (mttt) cc_final: 0.8322 (mttp) REVERT: M 83 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7253 (tm-30) REVERT: N 45 LYS cc_start: 0.8593 (mttt) cc_final: 0.8208 (mttt) REVERT: N 83 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7223 (tm-30) REVERT: O 50 HIS cc_start: 0.6790 (OUTLIER) cc_final: 0.5823 (m-70) REVERT: P 45 LYS cc_start: 0.8522 (mttt) cc_final: 0.8131 (mttm) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 0.0996 time to fit residues: 7.2934 Evaluate side-chains 53 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 50 HIS Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain K residue 50 HIS Chi-restraints excluded: chain M residue 50 HIS Chi-restraints excluded: chain O residue 50 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.139120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.110407 restraints weight = 4646.934| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.64 r_work: 0.3592 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.042 4180 Z= 0.377 Angle : 0.675 4.900 5660 Z= 0.385 Chirality : 0.058 0.191 750 Planarity : 0.003 0.016 700 Dihedral : 6.847 53.048 620 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.43 % Allowed : 3.57 % Favored : 95.00 % 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: -1.40 (0.29), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR J 39 PHE 0.011 0.003 PHE K 94 HIS 0.018 0.006 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00900 ( 4180) covalent geometry : angle 0.67516 ( 5660) hydrogen bonds : bond 0.04532 ( 161) hydrogen bonds : angle 5.34025 ( 516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.150 Fit side-chains REVERT: G 45 LYS cc_start: 0.8952 (mttt) cc_final: 0.8628 (mttm) REVERT: G 60 LYS cc_start: 0.8747 (tttt) cc_final: 0.8294 (tttt) REVERT: G 94 PHE cc_start: 0.8338 (p90) cc_final: 0.8136 (p90) REVERT: H 45 LYS cc_start: 0.8961 (mttt) cc_final: 0.8722 (mttt) REVERT: H 60 LYS cc_start: 0.8712 (tttt) cc_final: 0.8264 (tttp) REVERT: I 60 LYS cc_start: 0.8546 (tttt) cc_final: 0.8210 (tttp) REVERT: J 60 LYS cc_start: 0.8592 (tttt) cc_final: 0.8268 (tttp) REVERT: K 96 LYS cc_start: 0.6981 (mttt) cc_final: 0.6727 (mttp) REVERT: L 60 LYS cc_start: 0.8652 (tttt) cc_final: 0.8149 (tttt) REVERT: M 45 LYS cc_start: 0.8612 (mttt) cc_final: 0.8311 (mtpp) REVERT: M 96 LYS cc_start: 0.7042 (mttt) cc_final: 0.6456 (mttt) REVERT: N 45 LYS cc_start: 0.8562 (mttt) cc_final: 0.7888 (mtpt) REVERT: N 60 LYS cc_start: 0.8580 (tttt) cc_final: 0.8242 (tttt) REVERT: O 60 LYS cc_start: 0.8578 (tttt) cc_final: 0.8261 (tttp) REVERT: O 80 LYS cc_start: 0.8872 (tttt) cc_final: 0.8617 (tttp) REVERT: P 60 LYS cc_start: 0.8574 (tttt) cc_final: 0.8334 (tttp) REVERT: P 80 LYS cc_start: 0.8783 (tttt) cc_final: 0.8198 (ttpt) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.1426 time to fit residues: 9.4453 Evaluate side-chains 61 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.145565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.118089 restraints weight = 4637.043| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.54 r_work: 0.3715 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4180 Z= 0.104 Angle : 0.461 2.833 5660 Z= 0.265 Chirality : 0.053 0.131 750 Planarity : 0.002 0.009 700 Dihedral : 4.674 14.198 610 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.19 % Allowed : 4.52 % Favored : 94.29 % 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: -1.02 (0.31), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR N 39 PHE 0.009 0.002 PHE K 94 HIS 0.011 0.004 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 4180) covalent geometry : angle 0.46145 ( 5660) hydrogen bonds : bond 0.02324 ( 161) hydrogen bonds : angle 4.84045 ( 516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.140 Fit side-chains REVERT: G 45 LYS cc_start: 0.8981 (mttt) cc_final: 0.8557 (mttt) REVERT: G 60 LYS cc_start: 0.8650 (tttt) cc_final: 0.8233 (tttt) REVERT: G 83 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7481 (tm-30) REVERT: H 45 LYS cc_start: 0.8978 (mttt) cc_final: 0.8729 (mttt) REVERT: H 60 LYS cc_start: 0.8592 (tttt) cc_final: 0.8172 (tttp) REVERT: H 83 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7539 (tm-30) REVERT: I 60 LYS cc_start: 0.8401 (tttt) cc_final: 0.8110 (tttp) REVERT: I 83 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7819 (tp30) REVERT: J 60 LYS cc_start: 0.8504 (tttt) cc_final: 0.8187 (tttp) REVERT: K 60 LYS cc_start: 0.8543 (tttt) cc_final: 0.8287 (tttp) REVERT: K 96 LYS cc_start: 0.6985 (mttt) cc_final: 0.6746 (mttp) REVERT: L 60 LYS cc_start: 0.8437 (tttt) cc_final: 0.7996 (tttt) REVERT: L 83 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7654 (mp0) REVERT: M 45 LYS cc_start: 0.8605 (mttt) cc_final: 0.8176 (mtpp) REVERT: M 83 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7540 (mp0) REVERT: M 96 LYS cc_start: 0.7146 (mttt) cc_final: 0.6722 (mttt) REVERT: N 45 LYS cc_start: 0.8625 (mttt) cc_final: 0.8168 (mtpp) REVERT: N 60 LYS cc_start: 0.8569 (tttt) cc_final: 0.8254 (tttt) REVERT: O 45 LYS cc_start: 0.8565 (mttt) cc_final: 0.7931 (mtmt) REVERT: O 60 LYS cc_start: 0.8652 (tttt) cc_final: 0.8272 (tttp) REVERT: O 80 LYS cc_start: 0.8804 (tttt) cc_final: 0.8216 (ttpt) REVERT: P 45 LYS cc_start: 0.8466 (mttt) cc_final: 0.7909 (mtmt) REVERT: P 60 LYS cc_start: 0.8495 (tttt) cc_final: 0.8244 (tttp) REVERT: P 80 LYS cc_start: 0.8773 (tttt) cc_final: 0.8126 (ttpt) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.1151 time to fit residues: 8.0108 Evaluate side-chains 62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.141578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.113320 restraints weight = 4549.426| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.63 r_work: 0.3645 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4180 Z= 0.187 Angle : 0.505 3.351 5660 Z= 0.285 Chirality : 0.053 0.130 750 Planarity : 0.002 0.010 700 Dihedral : 4.735 13.992 610 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.43 % Allowed : 4.76 % Favored : 93.81 % 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: -0.94 (0.32), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR N 39 PHE 0.010 0.002 PHE K 94 HIS 0.009 0.004 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 4180) covalent geometry : angle 0.50474 ( 5660) hydrogen bonds : bond 0.03037 ( 161) hydrogen bonds : angle 4.95345 ( 516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.172 Fit side-chains REVERT: G 45 LYS cc_start: 0.8962 (mttt) cc_final: 0.8700 (mttm) REVERT: G 60 LYS cc_start: 0.8740 (tttt) cc_final: 0.8377 (tttt) REVERT: G 96 LYS cc_start: 0.7699 (mttt) cc_final: 0.7457 (mttt) REVERT: H 45 LYS cc_start: 0.8938 (mttt) cc_final: 0.8727 (mttt) REVERT: H 60 LYS cc_start: 0.8665 (tttt) cc_final: 0.8222 (tttp) REVERT: H 83 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7570 (tm-30) REVERT: I 60 LYS cc_start: 0.8401 (tttt) cc_final: 0.8089 (tttp) REVERT: I 83 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7988 (tp30) REVERT: J 60 LYS cc_start: 0.8513 (tttt) cc_final: 0.8167 (tttp) REVERT: K 60 LYS cc_start: 0.8448 (tttt) cc_final: 0.8154 (tttp) REVERT: K 96 LYS cc_start: 0.6940 (mttt) cc_final: 0.6552 (mttp) REVERT: L 60 LYS cc_start: 0.8371 (tttt) cc_final: 0.7894 (tttt) REVERT: M 45 LYS cc_start: 0.8519 (mttt) cc_final: 0.8102 (mtpp) REVERT: M 83 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7454 (mp0) REVERT: M 96 LYS cc_start: 0.7102 (mttt) cc_final: 0.6573 (mttt) REVERT: N 45 LYS cc_start: 0.8590 (mttt) cc_final: 0.7932 (mtpt) REVERT: N 60 LYS cc_start: 0.8457 (tttt) cc_final: 0.8092 (tttt) REVERT: N 83 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7257 (tp30) REVERT: O 60 LYS cc_start: 0.8588 (tttt) cc_final: 0.8177 (tttp) REVERT: O 80 LYS cc_start: 0.8749 (tttt) cc_final: 0.8405 (tttm) REVERT: P 60 LYS cc_start: 0.8454 (tttt) cc_final: 0.8200 (tttp) REVERT: P 80 LYS cc_start: 0.8809 (tttt) cc_final: 0.8143 (ttpt) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.1420 time to fit residues: 9.7694 Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.139013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.110861 restraints weight = 4602.039| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.58 r_work: 0.3608 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4180 Z= 0.252 Angle : 0.565 4.212 5660 Z= 0.316 Chirality : 0.054 0.137 750 Planarity : 0.002 0.011 700 Dihedral : 4.897 14.415 610 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.90 % Allowed : 4.29 % Favored : 93.81 % 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: -1.06 (0.32), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.80 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR N 39 PHE 0.011 0.002 PHE J 94 HIS 0.009 0.004 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 4180) covalent geometry : angle 0.56500 ( 5660) hydrogen bonds : bond 0.03574 ( 161) hydrogen bonds : angle 5.06604 ( 516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.158 Fit side-chains REVERT: G 45 LYS cc_start: 0.8989 (mttt) cc_final: 0.8684 (mttm) REVERT: G 60 LYS cc_start: 0.8710 (tttt) cc_final: 0.8338 (tttt) REVERT: G 96 LYS cc_start: 0.7762 (mttt) cc_final: 0.7509 (mttt) REVERT: H 45 LYS cc_start: 0.8958 (mttt) cc_final: 0.8757 (mttt) REVERT: H 60 LYS cc_start: 0.8674 (tttt) cc_final: 0.8247 (tttp) REVERT: H 83 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7591 (tm-30) REVERT: I 60 LYS cc_start: 0.8426 (tttt) cc_final: 0.8120 (tttm) REVERT: I 83 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7957 (tp30) REVERT: J 60 LYS cc_start: 0.8545 (tttt) cc_final: 0.8213 (tttp) REVERT: K 60 LYS cc_start: 0.8512 (tttt) cc_final: 0.8216 (tttp) REVERT: K 96 LYS cc_start: 0.7101 (mttt) cc_final: 0.6700 (mttp) REVERT: L 60 LYS cc_start: 0.8427 (tttt) cc_final: 0.7937 (tttt) REVERT: M 45 LYS cc_start: 0.8590 (mttt) cc_final: 0.8122 (mtpp) REVERT: M 83 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7608 (mp0) REVERT: M 96 LYS cc_start: 0.7162 (mttt) cc_final: 0.6657 (mttt) REVERT: N 45 LYS cc_start: 0.8629 (mttt) cc_final: 0.7949 (mtpt) REVERT: N 60 LYS cc_start: 0.8508 (tttt) cc_final: 0.8117 (tttt) REVERT: N 83 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7267 (tp30) REVERT: O 60 LYS cc_start: 0.8612 (tttt) cc_final: 0.8233 (tttp) REVERT: O 80 LYS cc_start: 0.8838 (tttt) cc_final: 0.8430 (tttm) REVERT: P 60 LYS cc_start: 0.8485 (tttt) cc_final: 0.8253 (tttp) REVERT: P 80 LYS cc_start: 0.8782 (tttt) cc_final: 0.8157 (ttpt) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.1577 time to fit residues: 10.5585 Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.141276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.112918 restraints weight = 4693.908| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.67 r_work: 0.3634 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4180 Z= 0.160 Angle : 0.492 3.398 5660 Z= 0.277 Chirality : 0.053 0.128 750 Planarity : 0.002 0.010 700 Dihedral : 4.541 13.967 610 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.43 % Allowed : 5.00 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.33), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR N 39 PHE 0.011 0.002 PHE J 94 HIS 0.007 0.004 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4180) covalent geometry : angle 0.49165 ( 5660) hydrogen bonds : bond 0.02833 ( 161) hydrogen bonds : angle 4.91324 ( 516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.159 Fit side-chains REVERT: G 45 LYS cc_start: 0.8912 (mttt) cc_final: 0.8595 (mttm) REVERT: G 60 LYS cc_start: 0.8735 (tttt) cc_final: 0.8377 (tttt) REVERT: G 83 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7378 (tm-30) REVERT: G 96 LYS cc_start: 0.7745 (mttt) cc_final: 0.7491 (mttt) REVERT: H 45 LYS cc_start: 0.8950 (mttt) cc_final: 0.8750 (mttt) REVERT: H 60 LYS cc_start: 0.8657 (tttt) cc_final: 0.8232 (tttp) REVERT: H 83 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7564 (tm-30) REVERT: I 60 LYS cc_start: 0.8395 (tttt) cc_final: 0.8100 (tttp) REVERT: I 83 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7820 (tp30) REVERT: J 60 LYS cc_start: 0.8501 (tttt) cc_final: 0.8173 (tttp) REVERT: K 60 LYS cc_start: 0.8436 (tttt) cc_final: 0.8153 (tttp) REVERT: K 96 LYS cc_start: 0.7097 (mttt) cc_final: 0.6683 (mttp) REVERT: L 60 LYS cc_start: 0.8347 (tttt) cc_final: 0.7839 (tttt) REVERT: L 83 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7691 (mp0) REVERT: M 45 LYS cc_start: 0.8580 (mttt) cc_final: 0.8141 (mtpp) REVERT: M 83 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7509 (mp0) REVERT: M 96 LYS cc_start: 0.7152 (mttt) cc_final: 0.6634 (mttt) REVERT: N 45 LYS cc_start: 0.8620 (mttt) cc_final: 0.7950 (mtpt) REVERT: N 60 LYS cc_start: 0.8478 (tttt) cc_final: 0.8100 (tttt) REVERT: O 60 LYS cc_start: 0.8616 (tttt) cc_final: 0.8210 (tttp) REVERT: O 80 LYS cc_start: 0.8801 (tttt) cc_final: 0.8365 (tttm) REVERT: P 60 LYS cc_start: 0.8437 (tttt) cc_final: 0.8189 (tttp) REVERT: P 80 LYS cc_start: 0.8811 (tttt) cc_final: 0.8156 (ttpt) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.1501 time to fit residues: 10.5026 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.139492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.111136 restraints weight = 4724.387| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.63 r_work: 0.3608 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4180 Z= 0.219 Angle : 0.541 3.950 5660 Z= 0.302 Chirality : 0.053 0.134 750 Planarity : 0.002 0.011 700 Dihedral : 4.693 14.043 610 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.67 % Allowed : 5.48 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.33), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR I 39 PHE 0.018 0.003 PHE L 94 HIS 0.009 0.004 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 4180) covalent geometry : angle 0.54110 ( 5660) hydrogen bonds : bond 0.03373 ( 161) hydrogen bonds : angle 4.98548 ( 516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.149 Fit side-chains REVERT: G 45 LYS cc_start: 0.8927 (mttt) cc_final: 0.8611 (mttm) REVERT: G 60 LYS cc_start: 0.8741 (tttt) cc_final: 0.8374 (tttt) REVERT: G 96 LYS cc_start: 0.7787 (mttt) cc_final: 0.7499 (mttt) REVERT: H 60 LYS cc_start: 0.8670 (tttt) cc_final: 0.8248 (tttp) REVERT: H 83 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7587 (tm-30) REVERT: I 60 LYS cc_start: 0.8405 (tttt) cc_final: 0.8111 (tttp) REVERT: I 83 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7955 (tp30) REVERT: J 60 LYS cc_start: 0.8529 (tttt) cc_final: 0.8200 (tttp) REVERT: K 60 LYS cc_start: 0.8481 (tttt) cc_final: 0.8213 (tttp) REVERT: K 96 LYS cc_start: 0.7077 (mttt) cc_final: 0.6662 (mttp) REVERT: L 60 LYS cc_start: 0.8554 (tttt) cc_final: 0.7831 (tptt) REVERT: M 45 LYS cc_start: 0.8660 (mttt) cc_final: 0.8166 (mtpp) REVERT: M 83 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7591 (mp0) REVERT: M 96 LYS cc_start: 0.7214 (mttt) cc_final: 0.6801 (mttt) REVERT: N 45 LYS cc_start: 0.8660 (mttt) cc_final: 0.7979 (mtpt) REVERT: N 60 LYS cc_start: 0.8519 (tttt) cc_final: 0.8136 (tttt) REVERT: O 60 LYS cc_start: 0.8611 (tttt) cc_final: 0.8231 (tttp) REVERT: O 80 LYS cc_start: 0.8817 (tttt) cc_final: 0.8374 (tttm) REVERT: P 60 LYS cc_start: 0.8457 (tttt) cc_final: 0.8217 (tttp) REVERT: P 80 LYS cc_start: 0.8826 (tttt) cc_final: 0.8183 (ttpt) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.1549 time to fit residues: 10.6905 Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.138455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.110434 restraints weight = 4681.828| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.54 r_work: 0.3599 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4180 Z= 0.274 Angle : 0.586 4.490 5660 Z= 0.326 Chirality : 0.055 0.137 750 Planarity : 0.002 0.012 700 Dihedral : 4.845 14.227 610 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.90 % Allowed : 5.95 % Favored : 92.14 % 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: -1.21 (0.32), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR I 39 PHE 0.018 0.003 PHE L 94 HIS 0.010 0.004 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00647 ( 4180) covalent geometry : angle 0.58645 ( 5660) hydrogen bonds : bond 0.03686 ( 161) hydrogen bonds : angle 5.04188 ( 516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.157 Fit side-chains REVERT: G 45 LYS cc_start: 0.8915 (mttt) cc_final: 0.8591 (mttm) REVERT: G 60 LYS cc_start: 0.8728 (tttt) cc_final: 0.8350 (tttt) REVERT: G 96 LYS cc_start: 0.7749 (mttt) cc_final: 0.7471 (mttt) REVERT: H 60 LYS cc_start: 0.8671 (tttt) cc_final: 0.8259 (tttp) REVERT: H 83 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7599 (tm-30) REVERT: I 60 LYS cc_start: 0.8419 (tttt) cc_final: 0.8127 (tttp) REVERT: I 83 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7813 (tp30) REVERT: J 60 LYS cc_start: 0.8542 (tttt) cc_final: 0.8242 (tttp) REVERT: K 60 LYS cc_start: 0.8511 (tttt) cc_final: 0.8260 (tttp) REVERT: K 96 LYS cc_start: 0.7077 (mttt) cc_final: 0.6692 (mttp) REVERT: L 60 LYS cc_start: 0.8596 (tttt) cc_final: 0.7859 (tptt) REVERT: M 45 LYS cc_start: 0.8619 (mttt) cc_final: 0.8163 (mtpp) REVERT: M 96 LYS cc_start: 0.7165 (mttt) cc_final: 0.6640 (mttt) REVERT: N 45 LYS cc_start: 0.8657 (mttt) cc_final: 0.7967 (mtpt) REVERT: N 60 LYS cc_start: 0.8556 (tttt) cc_final: 0.8135 (tttt) REVERT: O 60 LYS cc_start: 0.8619 (tttt) cc_final: 0.8252 (tttp) REVERT: O 80 LYS cc_start: 0.8822 (tttt) cc_final: 0.8441 (tttp) REVERT: P 60 LYS cc_start: 0.8460 (tttt) cc_final: 0.8219 (tttp) REVERT: P 80 LYS cc_start: 0.8830 (tttt) cc_final: 0.8201 (ttpt) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.1524 time to fit residues: 10.5476 Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.137931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.109451 restraints weight = 4746.802| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.63 r_work: 0.3587 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4180 Z= 0.289 Angle : 0.600 4.705 5660 Z= 0.332 Chirality : 0.055 0.139 750 Planarity : 0.002 0.012 700 Dihedral : 4.866 14.350 610 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.43 % Allowed : 6.90 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.32), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR I 39 PHE 0.015 0.003 PHE L 94 HIS 0.010 0.004 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00683 ( 4180) covalent geometry : angle 0.59958 ( 5660) hydrogen bonds : bond 0.03795 ( 161) hydrogen bonds : angle 5.07226 ( 516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.157 Fit side-chains REVERT: G 45 LYS cc_start: 0.8915 (mttt) cc_final: 0.8594 (mttm) REVERT: G 60 LYS cc_start: 0.8741 (tttt) cc_final: 0.8354 (tttt) REVERT: G 96 LYS cc_start: 0.7738 (mttt) cc_final: 0.7453 (mttt) REVERT: H 60 LYS cc_start: 0.8685 (tttt) cc_final: 0.8265 (tttp) REVERT: H 83 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7585 (tm-30) REVERT: I 60 LYS cc_start: 0.8422 (tttt) cc_final: 0.8133 (tttp) REVERT: I 83 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7824 (tp30) REVERT: J 60 LYS cc_start: 0.8544 (tttt) cc_final: 0.8238 (tttp) REVERT: K 60 LYS cc_start: 0.8523 (tttt) cc_final: 0.8269 (tttp) REVERT: K 96 LYS cc_start: 0.7046 (mttt) cc_final: 0.6663 (mttp) REVERT: L 60 LYS cc_start: 0.8698 (tttt) cc_final: 0.7954 (tptt) REVERT: M 45 LYS cc_start: 0.8611 (mttt) cc_final: 0.8144 (mtpp) REVERT: M 96 LYS cc_start: 0.7121 (mttt) cc_final: 0.6613 (mttt) REVERT: N 45 LYS cc_start: 0.8653 (mttt) cc_final: 0.7968 (mtpt) REVERT: N 60 LYS cc_start: 0.8597 (tttt) cc_final: 0.8175 (tttt) REVERT: O 60 LYS cc_start: 0.8627 (tttt) cc_final: 0.8250 (tttp) REVERT: O 80 LYS cc_start: 0.8863 (tttt) cc_final: 0.8483 (tttp) REVERT: P 60 LYS cc_start: 0.8473 (tttt) cc_final: 0.8232 (tttp) REVERT: P 80 LYS cc_start: 0.8833 (tttt) cc_final: 0.8199 (ttpt) outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.1468 time to fit residues: 10.2271 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.139882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.111544 restraints weight = 4582.076| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.65 r_work: 0.3618 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4180 Z= 0.174 Angle : 0.514 3.738 5660 Z= 0.287 Chirality : 0.053 0.128 750 Planarity : 0.002 0.010 700 Dihedral : 4.568 14.145 610 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.43 % Allowed : 6.90 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.33), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR N 39 PHE 0.014 0.002 PHE L 94 HIS 0.008 0.004 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 4180) covalent geometry : angle 0.51430 ( 5660) hydrogen bonds : bond 0.02968 ( 161) hydrogen bonds : angle 4.93497 ( 516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.191 Fit side-chains REVERT: G 45 LYS cc_start: 0.8909 (mttt) cc_final: 0.8606 (mttm) REVERT: G 60 LYS cc_start: 0.8765 (tttt) cc_final: 0.8394 (tttt) REVERT: G 83 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7388 (tm-30) REVERT: G 96 LYS cc_start: 0.7723 (mttt) cc_final: 0.7442 (mttt) REVERT: H 60 LYS cc_start: 0.8660 (tttt) cc_final: 0.8240 (tttp) REVERT: H 83 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7515 (tm-30) REVERT: I 60 LYS cc_start: 0.8397 (tttt) cc_final: 0.8096 (tttp) REVERT: I 83 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7670 (tp30) REVERT: J 60 LYS cc_start: 0.8498 (tttt) cc_final: 0.8190 (tttp) REVERT: K 60 LYS cc_start: 0.8438 (tttt) cc_final: 0.8191 (tttp) REVERT: K 96 LYS cc_start: 0.7007 (mttt) cc_final: 0.6626 (mttp) REVERT: L 60 LYS cc_start: 0.8627 (tttt) cc_final: 0.8072 (tttt) REVERT: L 83 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7689 (mp0) REVERT: M 45 LYS cc_start: 0.8574 (mttt) cc_final: 0.8121 (mtpp) REVERT: M 83 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7554 (mp0) REVERT: M 96 LYS cc_start: 0.7084 (mttt) cc_final: 0.6668 (mttt) REVERT: N 45 LYS cc_start: 0.8621 (mttt) cc_final: 0.7930 (mtpt) REVERT: N 60 LYS cc_start: 0.8518 (tttt) cc_final: 0.8085 (tttt) REVERT: O 60 LYS cc_start: 0.8623 (tttt) cc_final: 0.8240 (tttp) REVERT: O 80 LYS cc_start: 0.8816 (tttt) cc_final: 0.8360 (tttm) REVERT: P 60 LYS cc_start: 0.8447 (tttt) cc_final: 0.8200 (tttm) REVERT: P 80 LYS cc_start: 0.8817 (tttt) cc_final: 0.8178 (ttpt) outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.1548 time to fit residues: 10.8030 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.137885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.109693 restraints weight = 4664.011| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.55 r_work: 0.3587 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 4180 Z= 0.294 Angle : 0.608 4.858 5660 Z= 0.336 Chirality : 0.055 0.140 750 Planarity : 0.002 0.012 700 Dihedral : 4.896 14.352 610 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.67 % Allowed : 6.67 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.32), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR I 39 PHE 0.015 0.003 PHE L 94 HIS 0.010 0.004 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00695 ( 4180) covalent geometry : angle 0.60805 ( 5660) hydrogen bonds : bond 0.03910 ( 161) hydrogen bonds : angle 5.09204 ( 516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1180.63 seconds wall clock time: 20 minutes 53.90 seconds (1253.90 seconds total)