Starting phenix.real_space_refine on Sun Mar 10 17:51:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh2_16876/03_2024/8oh2_16876_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh2_16876/03_2024/8oh2_16876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh2_16876/03_2024/8oh2_16876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh2_16876/03_2024/8oh2_16876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh2_16876/03_2024/8oh2_16876_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh2_16876/03_2024/8oh2_16876_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 2232 2.51 5 N 684 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3702 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "F" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "G" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "H" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "Q" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "R" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "S" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "T" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "V" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "W" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "X" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "Y" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "Z" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "a" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "b" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "c" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "d" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "e" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "f" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "g" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "h" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "i" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "j" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 102 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 13, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 12} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.61 Number of scatterers: 3702 At special positions: 0 Unit cell: (153.9, 93.1, 35.15, 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 786 8.00 N 684 7.00 C 2232 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 - 3.50 Amino acid : False - 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: 1.61 Conformation dependent library (CDL) restraints added in 598.3 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 648 1.28 - 1.35: 648 1.35 - 1.41: 153 1.41 - 1.48: 531 1.48 - 1.54: 1692 Bond restraints: 3672 Sorted by residual: bond pdb=" C ACE d 349 " pdb=" O ACE d 349 " ideal model delta sigma weight residual 1.199 1.226 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C ACE X 349 " pdb=" O ACE X 349 " ideal model delta sigma weight residual 1.199 1.225 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C ACE L 349 " pdb=" O ACE L 349 " ideal model delta sigma weight residual 1.199 1.225 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C ACE j 349 " pdb=" O ACE j 349 " ideal model delta sigma weight residual 1.199 1.225 -0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C ACE R 349 " pdb=" O ACE R 349 " ideal model delta sigma weight residual 1.199 1.225 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 3667 not shown) Histogram of bond angle deviations from ideal: 105.91 - 110.99: 1743 110.99 - 116.06: 846 116.06 - 121.13: 1177 121.13 - 126.20: 1130 126.20 - 131.27: 36 Bond angle restraints: 4932 Sorted by residual: angle pdb=" C ILE O 354 " pdb=" N GLY O 355 " pdb=" CA GLY O 355 " ideal model delta sigma weight residual 119.94 121.47 -1.53 1.09e+00 8.42e-01 1.98e+00 angle pdb=" C ILE a 354 " pdb=" N GLY a 355 " pdb=" CA GLY a 355 " ideal model delta sigma weight residual 119.94 121.46 -1.52 1.09e+00 8.42e-01 1.96e+00 angle pdb=" C ILE U 354 " pdb=" N GLY U 355 " pdb=" CA GLY U 355 " ideal model delta sigma weight residual 119.94 121.45 -1.51 1.09e+00 8.42e-01 1.92e+00 angle pdb=" C ILE C 354 " pdb=" N GLY C 355 " pdb=" CA GLY C 355 " ideal model delta sigma weight residual 119.94 121.45 -1.51 1.09e+00 8.42e-01 1.91e+00 angle pdb=" C ILE g 354 " pdb=" N GLY g 355 " pdb=" CA GLY g 355 " ideal model delta sigma weight residual 119.94 121.43 -1.49 1.09e+00 8.42e-01 1.88e+00 ... (remaining 4927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.13: 1896 11.13 - 22.27: 198 22.27 - 33.40: 36 33.40 - 44.53: 36 44.53 - 55.66: 30 Dihedral angle restraints: 2196 sinusoidal: 900 harmonic: 1296 Sorted by residual: dihedral pdb=" CA ASN b 359 " pdb=" C ASN b 359 " pdb=" N ILE b 360 " pdb=" CA ILE b 360 " ideal model delta harmonic sigma weight residual 180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASN h 359 " pdb=" C ASN h 359 " pdb=" N ILE h 360 " pdb=" CA ILE h 360 " ideal model delta harmonic sigma weight residual -180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASN P 359 " pdb=" C ASN P 359 " pdb=" N ILE P 360 " pdb=" CA ILE P 360 " ideal model delta harmonic sigma weight residual -180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 2193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 258 0.021 - 0.042: 162 0.042 - 0.062: 104 0.062 - 0.083: 16 0.083 - 0.104: 72 Chirality restraints: 612 Sorted by residual: chirality pdb=" CA ILE Q 354 " pdb=" N ILE Q 354 " pdb=" C ILE Q 354 " pdb=" CB ILE Q 354 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.69e-01 chirality pdb=" CA ILE e 354 " pdb=" N ILE e 354 " pdb=" C ILE e 354 " pdb=" CB ILE e 354 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.67e-01 chirality pdb=" CA ILE E 354 " pdb=" N ILE E 354 " pdb=" C ILE E 354 " pdb=" CB ILE E 354 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.65e-01 ... (remaining 609 not shown) Planarity restraints: 648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN U 351 " -0.002 2.00e-02 2.50e+03 3.89e-03 1.51e-01 pdb=" C GLN U 351 " 0.007 2.00e-02 2.50e+03 pdb=" O GLN U 351 " -0.003 2.00e-02 2.50e+03 pdb=" N SER U 352 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN a 351 " 0.002 2.00e-02 2.50e+03 3.75e-03 1.41e-01 pdb=" C GLN a 351 " -0.006 2.00e-02 2.50e+03 pdb=" O GLN a 351 " 0.002 2.00e-02 2.50e+03 pdb=" N SER a 352 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN g 351 " -0.002 2.00e-02 2.50e+03 3.68e-03 1.35e-01 pdb=" C GLN g 351 " 0.006 2.00e-02 2.50e+03 pdb=" O GLN g 351 " -0.002 2.00e-02 2.50e+03 pdb=" N SER g 352 " -0.002 2.00e-02 2.50e+03 ... (remaining 645 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 191 2.75 - 3.29: 2988 3.29 - 3.83: 6233 3.83 - 4.36: 6694 4.36 - 4.90: 12119 Nonbonded interactions: 28225 Sorted by model distance: nonbonded pdb=" NE2 HIS I 362 " pdb=" O HOH I 401 " model vdw 2.219 2.520 nonbonded pdb=" NE2 HIS g 362 " pdb=" O HOH g 401 " model vdw 2.230 2.520 nonbonded pdb=" NE2 HIS U 362 " pdb=" O HOH U 401 " model vdw 2.240 2.520 nonbonded pdb=" O HIS C 362 " pdb=" N NH2 O 363 " model vdw 2.310 3.120 nonbonded pdb=" NE2 HIS O 362 " pdb=" O HOH O 401 " model vdw 2.341 2.520 ... (remaining 28220 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = 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' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } 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: 1.120 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: 5.160 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.790 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.007 0.034 3672 Z= 0.324 Angle : 0.618 4.537 4932 Z= 0.305 Chirality : 0.044 0.104 612 Planarity : 0.001 0.004 648 Dihedral : 13.000 55.661 1332 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.25), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.19), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS d 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.471 Fit side-chains REVERT: G 353 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8266 (tttt) REVERT: J 353 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7932 (ttpt) REVERT: K 353 LYS cc_start: 0.8336 (tttt) cc_final: 0.8126 (mtpp) REVERT: N 362 HIS cc_start: 0.7792 (t70) cc_final: 0.7580 (t70) REVERT: S 353 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8302 (tttt) REVERT: V 353 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7566 (mtpp) REVERT: X 360 ILE cc_start: 0.8251 (mt) cc_final: 0.7942 (OUTLIER) REVERT: b 353 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8127 (ttmm) REVERT: e 353 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8166 (tttt) REVERT: j 360 ILE cc_start: 0.8327 (mt) cc_final: 0.8075 (mm) outliers start: 0 outliers final: 1 residues processed: 123 average time/residue: 0.6640 time to fit residues: 85.5817 Evaluate side-chains 94 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 351 GLN S 351 GLN T 362 HIS X 359 ASN f 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3672 Z= 0.139 Angle : 0.551 8.608 4932 Z= 0.257 Chirality : 0.047 0.121 612 Planarity : 0.001 0.011 648 Dihedral : 15.061 58.785 504 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.70 % Allowed : 15.51 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.28), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.21), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS U 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.499 Fit side-chains REVERT: C 353 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7631 (tttp) REVERT: D 353 LYS cc_start: 0.8446 (ttpt) cc_final: 0.7995 (ttmm) REVERT: G 353 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8245 (tttt) REVERT: I 358 ASP cc_start: 0.8045 (m-30) cc_final: 0.7829 (m-30) REVERT: J 353 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7754 (ttpp) REVERT: K 362 HIS cc_start: 0.7678 (t70) cc_final: 0.7279 (t70) REVERT: P 353 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8014 (ttmm) REVERT: S 353 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8210 (tttt) REVERT: W 356 SER cc_start: 0.8570 (t) cc_final: 0.8309 (p) REVERT: e 353 LYS cc_start: 0.8504 (ttmt) cc_final: 0.8220 (tttt) outliers start: 16 outliers final: 9 residues processed: 110 average time/residue: 0.6546 time to fit residues: 75.8068 Evaluate side-chains 101 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain c residue 356 SER Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 0.0770 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 overall best weight: 7.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 351 GLN W 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 3672 Z= 0.294 Angle : 0.678 9.115 4932 Z= 0.325 Chirality : 0.047 0.119 612 Planarity : 0.002 0.007 648 Dihedral : 15.035 59.367 504 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.24 % Allowed : 19.68 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.29), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.23), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS j 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.497 Fit side-chains REVERT: G 353 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8319 (tttt) REVERT: I 358 ASP cc_start: 0.8075 (m-30) cc_final: 0.7778 (m-30) REVERT: J 353 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7761 (ttpp) REVERT: K 362 HIS cc_start: 0.7700 (t70) cc_final: 0.7402 (t70) REVERT: S 353 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8291 (tttt) REVERT: U 358 ASP cc_start: 0.7941 (m-30) cc_final: 0.7738 (m-30) REVERT: W 356 SER cc_start: 0.8612 (t) cc_final: 0.8398 (p) REVERT: e 353 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8256 (tttt) outliers start: 14 outliers final: 10 residues processed: 94 average time/residue: 0.7081 time to fit residues: 69.9029 Evaluate side-chains 94 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 34 optimal weight: 9.9990 chunk 17 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 3672 Z= 0.045 Angle : 0.444 8.087 4932 Z= 0.206 Chirality : 0.048 0.117 612 Planarity : 0.001 0.002 648 Dihedral : 14.791 59.840 504 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 20.60 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS g 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.487 Fit side-chains REVERT: G 353 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8257 (tttt) REVERT: J 353 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7730 (ttpp) REVERT: K 362 HIS cc_start: 0.7590 (t70) cc_final: 0.7317 (t70) REVERT: P 353 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8003 (ttmm) REVERT: S 353 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8176 (tttt) REVERT: W 353 LYS cc_start: 0.8384 (tttt) cc_final: 0.8167 (ttmt) REVERT: W 356 SER cc_start: 0.8524 (t) cc_final: 0.8181 (p) REVERT: e 353 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8135 (tttt) outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 0.6853 time to fit residues: 72.1301 Evaluate side-chains 94 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain c residue 361 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.0030 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 0.0770 chunk 24 optimal weight: 0.0010 chunk 17 optimal weight: 30.0000 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 3672 Z= 0.040 Angle : 0.428 8.007 4932 Z= 0.196 Chirality : 0.047 0.115 612 Planarity : 0.000 0.004 648 Dihedral : 14.495 59.998 504 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.93 % Allowed : 23.61 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.35), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS b 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.485 Fit side-chains REVERT: G 353 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8211 (tttt) REVERT: J 353 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7706 (ttpp) REVERT: K 362 HIS cc_start: 0.7507 (t70) cc_final: 0.7230 (t70) REVERT: P 353 LYS cc_start: 0.8533 (ttpt) cc_final: 0.7997 (ttmm) REVERT: S 353 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8180 (tttt) REVERT: W 353 LYS cc_start: 0.8356 (tttt) cc_final: 0.8146 (ttmt) REVERT: e 353 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8130 (tttt) outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 0.6671 time to fit residues: 68.8309 Evaluate side-chains 89 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain c residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 0.0060 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 overall best weight: 6.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Z 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3672 Z= 0.278 Angle : 0.652 9.599 4932 Z= 0.316 Chirality : 0.046 0.116 612 Planarity : 0.002 0.007 648 Dihedral : 14.999 59.911 504 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.47 % Allowed : 21.30 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.32), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS j 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.464 Fit side-chains REVERT: C 353 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7395 (tttt) REVERT: G 353 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8329 (tttt) REVERT: J 353 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7720 (ttpp) REVERT: K 362 HIS cc_start: 0.7660 (t70) cc_final: 0.7383 (t70) REVERT: S 353 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8293 (tttt) REVERT: W 356 SER cc_start: 0.8646 (t) cc_final: 0.8401 (p) REVERT: a 353 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7627 (tttp) REVERT: e 353 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8236 (tttt) outliers start: 15 outliers final: 11 residues processed: 96 average time/residue: 0.6844 time to fit residues: 69.0535 Evaluate side-chains 97 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain a residue 353 LYS Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 0.0020 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 overall best weight: 5.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3672 Z= 0.247 Angle : 0.628 9.589 4932 Z= 0.303 Chirality : 0.046 0.121 612 Planarity : 0.002 0.006 648 Dihedral : 15.029 59.820 504 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 4.17 % Allowed : 20.83 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.32), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS j 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.489 Fit side-chains REVERT: C 353 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7391 (tttt) REVERT: G 353 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8329 (tttt) REVERT: J 353 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7719 (ttpp) REVERT: K 362 HIS cc_start: 0.7714 (t70) cc_final: 0.7482 (t70) REVERT: S 353 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8268 (tttt) REVERT: W 356 SER cc_start: 0.8641 (t) cc_final: 0.8394 (p) REVERT: a 353 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7577 (tttp) REVERT: e 353 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8232 (tttt) REVERT: e 360 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9014 (mt) outliers start: 18 outliers final: 13 residues processed: 96 average time/residue: 0.6998 time to fit residues: 70.5899 Evaluate side-chains 100 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain T residue 357 LEU Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain a residue 353 LYS Chi-restraints excluded: chain c residue 353 LYS Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain e residue 360 ILE Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 30.0000 chunk 3 optimal weight: 0.0870 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 0.3980 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 0.0020 chunk 9 optimal weight: 0.0770 overall best weight: 1.3126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.021 3672 Z= 0.066 Angle : 0.492 9.062 4932 Z= 0.224 Chirality : 0.047 0.119 612 Planarity : 0.001 0.003 648 Dihedral : 14.814 59.992 504 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 22.69 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS b 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.413 Fit side-chains REVERT: G 353 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8275 (tttt) REVERT: I 358 ASP cc_start: 0.8000 (m-30) cc_final: 0.7797 (m-30) REVERT: J 353 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7734 (ttpp) REVERT: K 362 HIS cc_start: 0.7639 (t70) cc_final: 0.7411 (t70) REVERT: P 353 LYS cc_start: 0.8511 (ttpt) cc_final: 0.7981 (ttmm) REVERT: W 356 SER cc_start: 0.8503 (t) cc_final: 0.8204 (p) REVERT: a 353 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7407 (tttp) REVERT: e 353 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8150 (tttt) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.7144 time to fit residues: 70.4941 Evaluate side-chains 93 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain a residue 353 LYS Chi-restraints excluded: chain c residue 353 LYS Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 3672 Z= 0.262 Angle : 0.640 9.909 4932 Z= 0.309 Chirality : 0.046 0.122 612 Planarity : 0.002 0.006 648 Dihedral : 15.035 59.815 504 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.24 % Allowed : 21.76 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.32), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS j 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.482 Fit side-chains REVERT: G 353 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8324 (tttt) REVERT: J 353 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7752 (ttpp) REVERT: K 362 HIS cc_start: 0.7708 (t70) cc_final: 0.7489 (t70) REVERT: W 356 SER cc_start: 0.8624 (t) cc_final: 0.8372 (p) REVERT: a 353 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7608 (tttp) REVERT: e 353 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8233 (tttt) REVERT: e 360 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8993 (mt) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 0.7103 time to fit residues: 67.9776 Evaluate side-chains 93 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain a residue 353 LYS Chi-restraints excluded: chain c residue 353 LYS Chi-restraints excluded: chain c residue 356 SER Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain e residue 360 ILE Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3672 Z= 0.159 Angle : 0.553 9.675 4932 Z= 0.263 Chirality : 0.046 0.119 612 Planarity : 0.001 0.005 648 Dihedral : 14.972 59.673 504 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.78 % Allowed : 21.76 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.32), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS j 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.491 Fit side-chains REVERT: G 353 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8321 (tttt) REVERT: J 353 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7718 (ttpp) REVERT: K 362 HIS cc_start: 0.7690 (t70) cc_final: 0.7470 (t70) REVERT: P 353 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8024 (ttmm) REVERT: W 356 SER cc_start: 0.8607 (t) cc_final: 0.8341 (p) REVERT: a 353 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7534 (tttp) REVERT: e 353 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8210 (tttt) outliers start: 12 outliers final: 9 residues processed: 89 average time/residue: 0.7636 time to fit residues: 71.2164 Evaluate side-chains 92 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain T residue 356 SER Chi-restraints excluded: chain U residue 356 SER Chi-restraints excluded: chain a residue 353 LYS Chi-restraints excluded: chain c residue 356 SER Chi-restraints excluded: chain c residue 361 THR Chi-restraints excluded: chain d residue 361 THR Chi-restraints excluded: chain f residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.0870 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 24 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.6720 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.131931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101296 restraints weight = 4414.607| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.66 r_work: 0.3609 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3672 Z= 0.116 Angle : 0.520 9.595 4932 Z= 0.244 Chirality : 0.046 0.118 612 Planarity : 0.001 0.004 648 Dihedral : 14.901 59.966 504 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 1.62 % Allowed : 22.92 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS j 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.06 seconds wall clock time: 33 minutes 5.85 seconds (1985.85 seconds total)