Starting phenix.real_space_refine on Sat May 2 06:21:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ufs_64121/05_2026/9ufs_64121.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ufs_64121/05_2026/9ufs_64121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ufs_64121/05_2026/9ufs_64121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ufs_64121/05_2026/9ufs_64121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ufs_64121/05_2026/9ufs_64121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ufs_64121/05_2026/9ufs_64121.map" } resolution = 2.7 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 1644 2.51 5 N 456 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: D, E, F, B, C Time building chain proxies: 0.52, per 1000 atoms: 0.20 Number of scatterers: 2628 At special positions: 0 Unit cell: (102.09, 117.03, 30.71, 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 528 8.00 N 456 7.00 C 1644 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: 0.20 Conformation dependent library (CDL) restraints added in 119.7 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 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 10 sheets defined 0.0% alpha, 61.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.827A pdb=" N TYR A 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 66 removed outlier: 9.139A pdb=" N LYS A 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N VAL D 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY A 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N HIS D 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL D 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLY A 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N THR D 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ALA A 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N ALA D 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL A 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 9.788A pdb=" N LYS D 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLU A 57 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N LYS D 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A 59 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLN D 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL D 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU A 46 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY E 47 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA E 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR A 54 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL E 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA A 56 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU E 57 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 58 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR E 59 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 78 removed outlier: 6.744A pdb=" N VAL A 74 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR D 75 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA A 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N THR E 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL E 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLY A 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N ALA E 76 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N THR A 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ALA E 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 81 through 82 removed outlier: 6.847A pdb=" N THR A 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 86 through 92 removed outlier: 6.716A pdb=" N ALA D 90 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA A 91 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR D 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 86 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ALA E 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA E 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N ALA A 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.825A pdb=" N TYR F 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 66 removed outlier: 9.142A pdb=" N LYS F 45 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N VAL B 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY F 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N HIS B 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL F 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY F 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N THR B 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ALA F 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N ALA B 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N VAL F 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N LYS B 58 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N GLU F 57 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N LYS B 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR F 59 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLN B 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU F 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR B 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL F 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL B 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN F 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU F 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY C 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL F 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA C 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR F 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA F 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU C 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS F 58 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR C 59 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 78 removed outlier: 6.745A pdb=" N VAL F 74 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR B 75 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA F 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA F 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N THR C 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL F 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY F 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA C 76 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR F 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA C 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL F 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.848A pdb=" N THR F 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 86 through 92 removed outlier: 6.717A pdb=" N ALA B 90 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA F 91 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B 92 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY F 86 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ALA C 89 " --> pdb=" O GLY F 86 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ILE F 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA C 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ALA F 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 138 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: 0.27 Time building geometry restraints manager: 0.28 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: 408 1.35 - 1.41: 108 1.41 - 1.48: 433 1.48 - 1.54: 1229 Bond restraints: 2640 Sorted by residual: bond pdb=" CB VAL C 40 " pdb=" CG1 VAL C 40 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 bond pdb=" CB VAL D 40 " pdb=" CG1 VAL D 40 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 bond pdb=" CB VAL A 40 " pdb=" CG1 VAL A 40 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL B 40 " pdb=" CG1 VAL B 40 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL F 40 " pdb=" CG1 VAL F 40 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 3322 1.07 - 2.14: 218 2.14 - 3.21: 24 3.21 - 4.27: 0 4.27 - 5.34: 6 Bond angle restraints: 3570 Sorted by residual: angle pdb=" N GLY D 73 " pdb=" CA GLY D 73 " pdb=" C GLY D 73 " ideal model delta sigma weight residual 113.18 118.52 -5.34 2.37e+00 1.78e-01 5.08e+00 angle pdb=" N GLY F 73 " pdb=" CA GLY F 73 " pdb=" C GLY F 73 " ideal model delta sigma weight residual 113.18 118.50 -5.32 2.37e+00 1.78e-01 5.04e+00 angle pdb=" N GLY B 73 " pdb=" CA GLY B 73 " pdb=" C GLY B 73 " ideal model delta sigma weight residual 113.18 118.49 -5.31 2.37e+00 1.78e-01 5.02e+00 angle pdb=" N GLY C 73 " pdb=" CA GLY C 73 " pdb=" C GLY C 73 " ideal model delta sigma weight residual 113.18 118.48 -5.30 2.37e+00 1.78e-01 5.01e+00 angle pdb=" N GLY A 73 " pdb=" CA GLY A 73 " pdb=" C GLY A 73 " ideal model delta sigma weight residual 113.18 118.47 -5.29 2.37e+00 1.78e-01 4.99e+00 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.49: 1320 10.49 - 20.98: 150 20.98 - 31.46: 48 31.46 - 41.95: 18 41.95 - 52.44: 12 Dihedral angle restraints: 1548 sinusoidal: 522 harmonic: 1026 Sorted by residual: dihedral pdb=" CA SER D 42 " pdb=" C SER D 42 " pdb=" N LYS D 43 " pdb=" CA LYS D 43 " ideal model delta harmonic sigma weight residual -180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER E 42 " pdb=" C SER E 42 " pdb=" N LYS E 43 " pdb=" CA LYS E 43 " ideal model delta harmonic sigma weight residual -180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER F 42 " pdb=" C SER F 42 " pdb=" N LYS F 43 " pdb=" CA LYS F 43 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 153 0.026 - 0.052: 175 0.052 - 0.078: 50 0.078 - 0.104: 66 0.104 - 0.130: 24 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 50 " -0.010 2.00e-02 2.50e+03 8.63e-03 1.12e+00 pdb=" CG HIS C 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS C 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS C 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 50 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.010 2.00e-02 2.50e+03 8.59e-03 1.11e+00 pdb=" CG HIS F 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.003 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 D 50 " 0.010 2.00e-02 2.50e+03 8.58e-03 1.11e+00 pdb=" CG HIS D 50 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS D 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS D 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS D 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS D 50 " 0.002 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 842 2.85 - 3.36: 2285 3.36 - 3.88: 4045 3.88 - 4.39: 4323 4.39 - 4.90: 9384 Nonbonded interactions: 20879 Sorted by model distance: nonbonded pdb=" OE1 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.339 3.120 nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.340 3.120 nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.340 3.120 nonbonded pdb=" OE1 GLU B 46 " pdb=" NZ LYS B 80 " model vdw 2.340 3.120 nonbonded pdb=" OE1 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.340 3.120 ... (remaining 20874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'B' selection = chain 'C' } 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: 3.020 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.150 Find NCS groups from input model: 0.020 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.008 0.038 2640 Z= 0.353 Angle : 0.630 5.343 3570 Z= 0.351 Chirality : 0.054 0.130 468 Planarity : 0.002 0.009 444 Dihedral : 12.227 52.438 900 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.50 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR B 39 PHE 0.016 0.004 PHE A 94 HIS 0.007 0.005 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00812 ( 2640) covalent geometry : angle 0.62962 ( 3570) hydrogen bonds : bond 0.17419 ( 46) hydrogen bonds : angle 8.09783 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.103 Fit side-chains REVERT: B 60 LYS cc_start: 0.8261 (tttp) cc_final: 0.8048 (tptm) REVERT: C 97 LYS cc_start: 0.7124 (mttt) cc_final: 0.6716 (ttmm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.7204 time to fit residues: 33.0564 Evaluate side-chains 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN D 65 ASN D 79 GLN E 65 ASN F 65 ASN B 65 ASN B 79 GLN C 65 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.131373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101540 restraints weight = 3096.130| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.31 r_work: 0.3526 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2640 Z= 0.089 Angle : 0.480 4.053 3570 Z= 0.263 Chirality : 0.052 0.133 468 Planarity : 0.002 0.010 444 Dihedral : 3.905 11.140 378 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.44 % Allowed : 7.04 % Favored : 88.52 % 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: -3.40 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR F 39 PHE 0.006 0.002 PHE F 94 HIS 0.006 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00177 ( 2640) covalent geometry : angle 0.48004 ( 3570) hydrogen bonds : bond 0.01782 ( 46) hydrogen bonds : angle 5.91404 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.108 Fit side-chains REVERT: B 60 LYS cc_start: 0.8633 (tttp) cc_final: 0.8382 (tptm) outliers start: 12 outliers final: 4 residues processed: 44 average time/residue: 0.6733 time to fit residues: 30.2076 Evaluate side-chains 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 33 optimal weight: 0.0770 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.126097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.096248 restraints weight = 3174.060| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.33 r_work: 0.3436 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2640 Z= 0.190 Angle : 0.536 4.572 3570 Z= 0.293 Chirality : 0.052 0.136 468 Planarity : 0.002 0.010 444 Dihedral : 4.302 12.237 378 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.07 % Allowed : 7.04 % Favored : 88.89 % 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: -3.04 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR E 39 PHE 0.012 0.003 PHE F 94 HIS 0.007 0.004 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 2640) covalent geometry : angle 0.53642 ( 3570) hydrogen bonds : bond 0.02421 ( 46) hydrogen bonds : angle 5.91200 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.077 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 36 average time/residue: 0.8696 time to fit residues: 31.8313 Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.126941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.097082 restraints weight = 3127.326| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.33 r_work: 0.3449 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2640 Z= 0.185 Angle : 0.524 4.533 3570 Z= 0.288 Chirality : 0.052 0.135 468 Planarity : 0.002 0.011 444 Dihedral : 4.331 12.505 378 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.81 % Allowed : 7.78 % Favored : 87.41 % 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: -2.82 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR F 39 PHE 0.012 0.003 PHE A 94 HIS 0.007 0.004 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 2640) covalent geometry : angle 0.52351 ( 3570) hydrogen bonds : bond 0.02345 ( 46) hydrogen bonds : angle 5.91781 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.101 Fit side-chains REVERT: E 87 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8325 (p) outliers start: 13 outliers final: 12 residues processed: 36 average time/residue: 0.7438 time to fit residues: 27.2879 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.129154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.099062 restraints weight = 3094.096| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.33 r_work: 0.3479 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2640 Z= 0.122 Angle : 0.466 4.148 3570 Z= 0.259 Chirality : 0.051 0.132 468 Planarity : 0.002 0.012 444 Dihedral : 4.002 12.043 378 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.81 % Allowed : 7.04 % Favored : 88.15 % 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: -2.58 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.009 0.002 PHE A 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2640) covalent geometry : angle 0.46632 ( 3570) hydrogen bonds : bond 0.01957 ( 46) hydrogen bonds : angle 5.76698 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.061 Fit side-chains REVERT: E 87 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8324 (p) outliers start: 13 outliers final: 12 residues processed: 36 average time/residue: 0.7131 time to fit residues: 26.2048 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.126976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.096581 restraints weight = 3137.074| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.36 r_work: 0.3445 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2640 Z= 0.191 Angle : 0.512 4.546 3570 Z= 0.284 Chirality : 0.051 0.135 468 Planarity : 0.002 0.012 444 Dihedral : 4.298 12.519 378 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.81 % Allowed : 8.15 % Favored : 87.04 % 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: -2.53 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR F 39 PHE 0.013 0.003 PHE A 94 HIS 0.007 0.004 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 2640) covalent geometry : angle 0.51189 ( 3570) hydrogen bonds : bond 0.02350 ( 46) hydrogen bonds : angle 5.96030 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.105 Fit side-chains REVERT: E 87 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8319 (p) outliers start: 13 outliers final: 12 residues processed: 36 average time/residue: 0.7436 time to fit residues: 27.3149 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 0.0030 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.127315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.099039 restraints weight = 3327.142| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.33 r_work: 0.3467 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2640 Z= 0.135 Angle : 0.470 4.226 3570 Z= 0.262 Chirality : 0.051 0.134 468 Planarity : 0.002 0.012 444 Dihedral : 4.047 12.339 378 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.81 % Allowed : 8.52 % Favored : 86.67 % 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: -2.39 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.010 0.003 PHE A 94 HIS 0.007 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2640) covalent geometry : angle 0.47011 ( 3570) hydrogen bonds : bond 0.02037 ( 46) hydrogen bonds : angle 5.79656 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.061 Fit side-chains REVERT: E 87 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8288 (p) outliers start: 13 outliers final: 12 residues processed: 36 average time/residue: 0.7281 time to fit residues: 26.7184 Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.129817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101330 restraints weight = 3366.087| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.34 r_work: 0.3505 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2640 Z= 0.090 Angle : 0.427 3.909 3570 Z= 0.240 Chirality : 0.051 0.131 468 Planarity : 0.002 0.013 444 Dihedral : 3.718 11.677 378 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.96 % Allowed : 10.37 % Favored : 86.67 % 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: -2.23 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR F 39 PHE 0.008 0.002 PHE A 94 HIS 0.006 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 2640) covalent geometry : angle 0.42694 ( 3570) hydrogen bonds : bond 0.01764 ( 46) hydrogen bonds : angle 5.53823 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.102 Fit side-chains REVERT: E 87 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8435 (p) REVERT: C 87 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8378 (p) outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.7362 time to fit residues: 25.5514 Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.129978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.101323 restraints weight = 3365.670| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.35 r_work: 0.3508 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2640 Z= 0.094 Angle : 0.423 3.853 3570 Z= 0.239 Chirality : 0.051 0.131 468 Planarity : 0.002 0.015 444 Dihedral : 3.672 11.442 378 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.96 % Allowed : 11.48 % Favored : 85.56 % 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: -2.14 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR F 39 PHE 0.008 0.002 PHE A 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 2640) covalent geometry : angle 0.42313 ( 3570) hydrogen bonds : bond 0.01759 ( 46) hydrogen bonds : angle 5.48946 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.123 Fit side-chains REVERT: E 87 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8447 (p) REVERT: C 87 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8415 (p) outliers start: 8 outliers final: 6 residues processed: 32 average time/residue: 0.7413 time to fit residues: 24.2101 Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.127645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098994 restraints weight = 3354.737| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.34 r_work: 0.3471 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2640 Z= 0.133 Angle : 0.455 4.037 3570 Z= 0.256 Chirality : 0.051 0.133 468 Planarity : 0.002 0.014 444 Dihedral : 3.928 11.961 378 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.33 % Allowed : 11.48 % Favored : 85.19 % 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: -2.15 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR F 39 PHE 0.010 0.002 PHE A 94 HIS 0.007 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2640) covalent geometry : angle 0.45494 ( 3570) hydrogen bonds : bond 0.01961 ( 46) hydrogen bonds : angle 5.67767 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.081 Fit side-chains REVERT: E 87 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8430 (p) outliers start: 9 outliers final: 8 residues processed: 32 average time/residue: 0.7191 time to fit residues: 23.4800 Evaluate side-chains 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.1244 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.129960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101124 restraints weight = 3299.330| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.35 r_work: 0.3510 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2640 Z= 0.092 Angle : 0.424 3.886 3570 Z= 0.239 Chirality : 0.051 0.131 468 Planarity : 0.002 0.015 444 Dihedral : 3.663 11.456 378 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.70 % Allowed : 11.48 % Favored : 84.81 % 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: -2.11 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR F 39 PHE 0.008 0.002 PHE A 94 HIS 0.006 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 2640) covalent geometry : angle 0.42369 ( 3570) hydrogen bonds : bond 0.01747 ( 46) hydrogen bonds : angle 5.46151 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1304.09 seconds wall clock time: 23 minutes 1.75 seconds (1381.75 seconds total)