Starting phenix.real_space_refine on Mon Jul 6 10:20:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjr_54951/07_2026/9sjr_54951_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjr_54951/07_2026/9sjr_54951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sjr_54951/07_2026/9sjr_54951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjr_54951/07_2026/9sjr_54951.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjr_54951/07_2026/9sjr_54951_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjr_54951/07_2026/9sjr_54951_neut.cif" } resolution = 1.99 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= 0.002 sd= 0.273 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: 6 Type Number sf(0) Gaussians Fe 24 7.16 5 Mg 24 5.21 5 S 168 5.16 5 C 21312 2.51 5 N 5952 2.21 5 O 7536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35016 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "B" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 1 Ad-hoc single atom residues: {' FE': 4} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 4 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "L" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "P" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "T" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "V" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "X" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Restraints were copied for chains: D, F, I, J, R, C, E, G, H, K, L, M, N, O, P, Q, S, T, V, W, X, Y Residues with excluded nonbonded symmetry interactions: 48 residue: pdb="FE FE A 201 " occ=0.25 residue: pdb="FE FE A 203 " occ=0.25 residue: pdb="FE FE A 204 " occ=0.25 residue: pdb="FE FE A 205 " occ=0.25 residue: pdb="FE FE D 201 " occ=0.25 residue: pdb="FE FE D 203 " occ=0.25 residue: pdb="FE FE D 204 " occ=0.25 residue: pdb="FE FE D 205 " occ=0.25 residue: pdb="FE FE F 201 " occ=0.25 residue: pdb="FE FE F 203 " occ=0.25 residue: pdb="FE FE F 204 " occ=0.25 residue: pdb="FE FE F 205 " occ=0.25 ... (remaining 36 not shown) Time building chain proxies: 4.06, per 1000 atoms: 0.12 Number of scatterers: 35016 At special positions: 0 Unit cell: (134.384, 134.384, 134.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 24 26.01 S 168 16.00 Mg 24 11.99 O 7536 8.00 N 5952 7.00 C 21312 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: 3.18 Conformation dependent library (CDL) restraints added in 1.3 seconds 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 Processing helix chain 'A' and resid 45 through 73 Processing helix chain 'A' and resid 92 through 121 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 38 Processing helix chain 'B' and resid 45 through 73 Processing helix chain 'B' and resid 92 through 121 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 38 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 92 through 121 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 38 Processing helix chain 'D' and resid 45 through 73 Processing helix chain 'D' and resid 92 through 121 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 38 Processing helix chain 'E' and resid 45 through 73 Processing helix chain 'E' and resid 92 through 121 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 134 through 156 Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 38 Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 121 Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 134 through 156 Processing helix chain 'F' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 38 Processing helix chain 'G' and resid 45 through 73 Processing helix chain 'G' and resid 92 through 121 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 134 through 156 Processing helix chain 'G' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 38 Processing helix chain 'H' and resid 45 through 73 Processing helix chain 'H' and resid 92 through 121 Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 134 through 156 Processing helix chain 'H' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU H 164 " --> pdb=" O SER H 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 38 Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 92 through 121 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 38 Processing helix chain 'J' and resid 45 through 73 Processing helix chain 'J' and resid 92 through 121 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU J 164 " --> pdb=" O SER J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 38 Processing helix chain 'K' and resid 45 through 73 Processing helix chain 'K' and resid 92 through 121 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 134 through 156 Processing helix chain 'K' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU K 164 " --> pdb=" O SER K 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 38 Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 121 Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 156 Processing helix chain 'L' and resid 160 through 171 removed outlier: 3.573A pdb=" N GLU L 164 " --> pdb=" O SER L 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 38 Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'M' and resid 92 through 121 Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 134 through 156 Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.572A pdb=" N GLU M 164 " --> pdb=" O SER M 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 38 Processing helix chain 'N' and resid 45 through 73 Processing helix chain 'N' and resid 92 through 121 Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 156 Processing helix chain 'N' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU N 164 " --> pdb=" O SER N 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 38 Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 121 Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 156 Processing helix chain 'O' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU O 164 " --> pdb=" O SER O 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 38 Processing helix chain 'P' and resid 45 through 73 Processing helix chain 'P' and resid 92 through 121 Processing helix chain 'P' and resid 123 through 134 Processing helix chain 'P' and resid 134 through 156 Processing helix chain 'P' and resid 160 through 171 removed outlier: 3.573A pdb=" N GLU P 164 " --> pdb=" O SER P 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 38 Processing helix chain 'Q' and resid 45 through 73 Processing helix chain 'Q' and resid 92 through 121 Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 156 Processing helix chain 'Q' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU Q 164 " --> pdb=" O SER Q 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 38 Processing helix chain 'R' and resid 45 through 73 Processing helix chain 'R' and resid 92 through 121 Processing helix chain 'R' and resid 123 through 134 Processing helix chain 'R' and resid 134 through 156 Processing helix chain 'R' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 38 Processing helix chain 'S' and resid 45 through 73 Processing helix chain 'S' and resid 92 through 121 Processing helix chain 'S' and resid 123 through 134 Processing helix chain 'S' and resid 134 through 156 Processing helix chain 'S' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU S 164 " --> pdb=" O SER S 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 38 Processing helix chain 'T' and resid 45 through 73 Processing helix chain 'T' and resid 92 through 121 Processing helix chain 'T' and resid 123 through 134 Processing helix chain 'T' and resid 134 through 156 Processing helix chain 'T' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU T 164 " --> pdb=" O SER T 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 38 Processing helix chain 'V' and resid 45 through 73 Processing helix chain 'V' and resid 92 through 121 Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 156 Processing helix chain 'V' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU V 164 " --> pdb=" O SER V 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 38 Processing helix chain 'W' and resid 45 through 73 Processing helix chain 'W' and resid 92 through 121 Processing helix chain 'W' and resid 123 through 134 Processing helix chain 'W' and resid 134 through 156 Processing helix chain 'W' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU W 164 " --> pdb=" O SER W 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 38 Processing helix chain 'X' and resid 45 through 73 Processing helix chain 'X' and resid 92 through 121 Processing helix chain 'X' and resid 123 through 134 Processing helix chain 'X' and resid 134 through 156 Processing helix chain 'X' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU X 164 " --> pdb=" O SER X 160 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 38 Processing helix chain 'Y' and resid 45 through 73 Processing helix chain 'Y' and resid 92 through 121 Processing helix chain 'Y' and resid 123 through 134 Processing helix chain 'Y' and resid 134 through 156 Processing helix chain 'Y' and resid 160 through 171 removed outlier: 3.574A pdb=" N GLU Y 164 " --> pdb=" O SER Y 160 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7920 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: 6.37 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11550 1.34 - 1.46: 5447 1.46 - 1.58: 17443 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34704 Sorted by residual: bond pdb=" C ASN C 18 " pdb=" O ASN C 18 " ideal model delta sigma weight residual 1.237 1.245 -0.009 1.17e-02 7.31e+03 5.66e-01 bond pdb=" C ASN P 18 " pdb=" O ASN P 18 " ideal model delta sigma weight residual 1.237 1.245 -0.009 1.17e-02 7.31e+03 5.64e-01 bond pdb=" C ASN L 18 " pdb=" O ASN L 18 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.17e-02 7.31e+03 5.21e-01 bond pdb=" C ASN R 18 " pdb=" O ASN R 18 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.17e-02 7.31e+03 5.21e-01 bond pdb=" C ASN N 18 " pdb=" O ASN N 18 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.17e-02 7.31e+03 5.09e-01 ... (remaining 34699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 45468 1.24 - 2.48: 906 2.48 - 3.72: 162 3.72 - 4.96: 144 4.96 - 6.20: 48 Bond angle restraints: 46728 Sorted by residual: angle pdb=" N GLU G 91 " pdb=" CA GLU G 91 " pdb=" C GLU G 91 " ideal model delta sigma weight residual 110.80 117.00 -6.20 2.13e+00 2.20e-01 8.48e+00 angle pdb=" N GLU X 91 " pdb=" CA GLU X 91 " pdb=" C GLU X 91 " ideal model delta sigma weight residual 110.80 117.00 -6.20 2.13e+00 2.20e-01 8.46e+00 angle pdb=" N GLU T 91 " pdb=" CA GLU T 91 " pdb=" C GLU T 91 " ideal model delta sigma weight residual 110.80 117.00 -6.20 2.13e+00 2.20e-01 8.46e+00 angle pdb=" N GLU B 91 " pdb=" CA GLU B 91 " pdb=" C GLU B 91 " ideal model delta sigma weight residual 110.80 117.00 -6.20 2.13e+00 2.20e-01 8.46e+00 angle pdb=" N GLU R 91 " pdb=" CA GLU R 91 " pdb=" C GLU R 91 " ideal model delta sigma weight residual 110.80 117.00 -6.20 2.13e+00 2.20e-01 8.46e+00 ... (remaining 46723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 18648 17.75 - 35.49: 1652 35.49 - 53.24: 508 53.24 - 70.99: 96 70.99 - 88.73: 96 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA TRP J 90 " pdb=" C TRP J 90 " pdb=" N GLU J 91 " pdb=" CA GLU J 91 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA TRP Y 90 " pdb=" C TRP Y 90 " pdb=" N GLU Y 91 " pdb=" CA GLU Y 91 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA TRP S 90 " pdb=" C TRP S 90 " pdb=" N GLU S 91 " pdb=" CA GLU S 91 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3056 0.027 - 0.053: 1142 0.053 - 0.080: 460 0.080 - 0.107: 193 0.107 - 0.134: 69 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR L 36 " pdb=" N TYR L 36 " pdb=" C TYR L 36 " pdb=" CB TYR L 36 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA TYR M 36 " pdb=" N TYR M 36 " pdb=" C TYR M 36 " pdb=" CB TYR M 36 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA TYR P 36 " pdb=" N TYR P 36 " pdb=" C TYR P 36 " pdb=" CB TYR P 36 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 4917 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 36 " 0.016 2.00e-02 2.50e+03 9.53e-03 1.82e+00 pdb=" CG TYR J 36 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR J 36 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR J 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR J 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR J 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR J 36 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR J 36 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 36 " 0.016 2.00e-02 2.50e+03 9.52e-03 1.81e+00 pdb=" CG TYR D 36 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D 36 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 36 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 36 " 0.016 2.00e-02 2.50e+03 9.51e-03 1.81e+00 pdb=" CG TYR F 36 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR F 36 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR F 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 36 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 36 " 0.003 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 72 0.98 - 1.96: 0 1.96 - 2.94: 15877 2.94 - 3.92: 110108 3.92 - 4.90: 194902 Warning: very small nonbonded interaction distances. Nonbonded interactions: 320959 Sorted by model distance: nonbonded pdb=" O HOH T 340 " pdb=" O HOH V 340 " model vdw 0.004 3.040 nonbonded pdb=" O HOH T 339 " pdb=" O HOH V 339 " model vdw 0.004 3.040 nonbonded pdb="FE FE F 201 " pdb="FE FE F 204 " model vdw 0.004 2.960 nonbonded pdb="FE FE R 204 " pdb="FE FE R 205 " model vdw 0.004 2.960 nonbonded pdb=" O HOH X 341 " pdb=" O HOH X 342 " model vdw 0.004 3.040 ... (remaining 320954 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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=0.25 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: 3.190 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: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.280 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 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 : 0.003 0.020 34704 Z= 0.145 Angle : 0.541 6.202 46728 Z= 0.300 Chirality : 0.037 0.134 4920 Planarity : 0.004 0.039 6144 Dihedral : 16.400 88.735 13032 Min Nonbonded Distance : 0.004 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.30 % Allowed : 5.19 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.30 (0.13), residues: 4104 helix: 4.04 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.19 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 60 TYR 0.021 0.002 TYR F 36 PHE 0.019 0.002 PHE J 38 TRP 0.010 0.003 TRP R 90 HIS 0.008 0.001 HIS Y 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (34704) covalent geometry : angle 0.54121 / 0.30 (46728) hydrogen bonds : bond 0.08196 / 5.44 ( 2640) hydrogen bonds : angle 3.92093 / 2.82 ( 7920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 720 time to evaluate : 1.645 Fit side-chains outliers start: 48 outliers final: 24 residues processed: 744 average time/residue: 0.8909 time to fit residues: 764.3545 Evaluate side-chains 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 696 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain F residue 1 SER Chi-restraints excluded: chain G residue 1 SER Chi-restraints excluded: chain H residue 1 SER Chi-restraints excluded: chain I residue 1 SER Chi-restraints excluded: chain J residue 1 SER Chi-restraints excluded: chain K residue 1 SER Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain M residue 1 SER Chi-restraints excluded: chain N residue 1 SER Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain Q residue 1 SER Chi-restraints excluded: chain R residue 1 SER Chi-restraints excluded: chain S residue 1 SER Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain V residue 1 SER Chi-restraints excluded: chain W residue 1 SER Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain Y residue 1 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 72 GLN A 80 GLN B 22 ASN B 72 GLN B 80 GLN C 22 ASN C 72 GLN C 80 GLN D 22 ASN D 72 GLN D 80 GLN E 22 ASN E 72 GLN E 80 GLN F 22 ASN F 72 GLN F 80 GLN G 22 ASN G 72 GLN G 80 GLN H 22 ASN H 72 GLN H 80 GLN I 22 ASN I 72 GLN I 80 GLN J 22 ASN J 72 GLN J 80 GLN K 22 ASN K 72 GLN K 80 GLN L 22 ASN L 72 GLN L 80 GLN M 22 ASN M 72 GLN M 80 GLN N 22 ASN N 72 GLN N 80 GLN O 22 ASN O 72 GLN O 80 GLN P 22 ASN P 72 GLN P 80 GLN Q 22 ASN Q 72 GLN Q 80 GLN R 22 ASN R 72 GLN R 80 GLN S 22 ASN S 72 GLN S 80 GLN T 22 ASN T 72 GLN T 80 GLN V 22 ASN V 72 GLN V 80 GLN W 22 ASN W 72 GLN W 80 GLN X 22 ASN X 72 GLN X 80 GLN Y 22 ASN Y 72 GLN Y 80 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.128351 restraints weight = 24689.842| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 0.67 r_work: 0.3289 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.2916 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 34704 Z= 0.112 Angle : 0.473 5.576 46728 Z= 0.262 Chirality : 0.035 0.124 4920 Planarity : 0.003 0.024 6144 Dihedral : 4.092 19.400 4536 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.50 (0.13), residues: 4104 helix: 4.12 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.30 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 60 TYR 0.017 0.002 TYR F 36 PHE 0.015 0.002 PHE F 38 TRP 0.009 0.002 TRP S 90 HIS 0.005 0.001 HIS D 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.11 (34704) covalent geometry : angle 0.47330 / 0.26 (46728) hydrogen bonds : bond 0.04760 / 3.19 ( 2640) hydrogen bonds : angle 3.37929 / 2.43 ( 7920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 717 time to evaluate : 1.235 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 717 average time/residue: 0.9439 time to fit residues: 777.8944 Evaluate side-chains 686 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 686 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 126 optimal weight: 9.9990 chunk 204 optimal weight: 40.0000 chunk 328 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 391 optimal weight: 0.0050 chunk 69 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 overall best weight: 5.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN B 80 GLN C 80 GLN D 80 GLN E 72 GLN E 80 GLN F 80 GLN G 72 GLN G 80 GLN H 80 GLN I 80 GLN J 80 GLN K 72 GLN K 80 GLN L 80 GLN M 72 GLN M 80 GLN N 80 GLN O 80 GLN P 72 GLN P 80 GLN Q 80 GLN R 80 GLN S 80 GLN T 80 GLN V 80 GLN W 80 GLN X 72 GLN X 80 GLN Y 72 GLN Y 80 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.136036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.123452 restraints weight = 24512.094| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 0.66 r_work: 0.3188 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.2805 rms_B_bonded: 4.54 restraints_weight: 0.1250 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34704 Z= 0.166 Angle : 0.574 6.725 46728 Z= 0.322 Chirality : 0.039 0.133 4920 Planarity : 0.004 0.033 6144 Dihedral : 4.183 19.180 4512 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.19 % Allowed : 5.01 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.12 (0.13), residues: 4104 helix: 3.89 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.13 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 60 TYR 0.022 0.003 TYR V 36 PHE 0.019 0.003 PHE S 38 TRP 0.014 0.004 TRP L 90 HIS 0.006 0.002 HIS R 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (34704) covalent geometry : angle 0.57425 / 0.32 (46728) hydrogen bonds : bond 0.06099 / 4.09 ( 2640) hydrogen bonds : angle 3.62324 / 2.61 ( 7920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 695 time to evaluate : 1.383 Fit side-chains REVERT: A 89 ASP cc_start: 0.7897 (t70) cc_final: 0.7507 (t70) REVERT: B 89 ASP cc_start: 0.7899 (t70) cc_final: 0.7498 (t70) REVERT: C 89 ASP cc_start: 0.7900 (t70) cc_final: 0.7507 (t70) REVERT: D 89 ASP cc_start: 0.7907 (t70) cc_final: 0.7534 (t70) REVERT: D 91 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8149 (mm-30) REVERT: H 89 ASP cc_start: 0.7906 (t70) cc_final: 0.7517 (t70) REVERT: I 89 ASP cc_start: 0.7900 (t70) cc_final: 0.7527 (t70) REVERT: I 91 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8148 (mm-30) REVERT: J 89 ASP cc_start: 0.7894 (t70) cc_final: 0.7528 (t70) REVERT: J 91 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8144 (mm-30) REVERT: M 89 ASP cc_start: 0.7894 (t70) cc_final: 0.7503 (t70) REVERT: N 89 ASP cc_start: 0.7911 (t70) cc_final: 0.7530 (t70) REVERT: N 91 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8145 (mm-30) REVERT: O 89 ASP cc_start: 0.7911 (t70) cc_final: 0.7535 (t70) REVERT: O 91 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8153 (mm-30) REVERT: Q 89 ASP cc_start: 0.7891 (t70) cc_final: 0.7498 (t70) REVERT: Q 91 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8141 (mm-30) REVERT: W 89 ASP cc_start: 0.7900 (t70) cc_final: 0.7527 (t70) REVERT: W 91 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8143 (mm-30) outliers start: 44 outliers final: 0 residues processed: 715 average time/residue: 0.9298 time to fit residues: 763.5798 Evaluate side-chains 695 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 286 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 405 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 317 optimal weight: 20.0000 chunk 271 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 80 GLN B 72 GLN B 80 GLN C 72 GLN C 80 GLN D 72 GLN D 80 GLN E 72 GLN E 80 GLN F 72 GLN F 80 GLN G 72 GLN G 80 GLN H 72 GLN H 80 GLN I 72 GLN I 80 GLN J 72 GLN J 80 GLN K 72 GLN K 80 GLN L 72 GLN L 80 GLN M 72 GLN M 80 GLN N 72 GLN N 80 GLN O 72 GLN O 80 GLN P 72 GLN P 80 GLN Q 72 GLN Q 80 GLN R 72 GLN R 80 GLN S 72 GLN S 80 GLN T 72 GLN T 80 GLN V 72 GLN V 80 GLN W 72 GLN W 80 GLN X 72 GLN X 80 GLN Y 72 GLN Y 80 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.124041 restraints weight = 24314.392| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 0.64 r_work: 0.3217 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.2836 rms_B_bonded: 4.50 restraints_weight: 0.1250 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34704 Z= 0.153 Angle : 0.552 6.478 46728 Z= 0.309 Chirality : 0.038 0.135 4920 Planarity : 0.004 0.027 6144 Dihedral : 4.169 18.748 4512 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.13 (0.13), residues: 4104 helix: 3.91 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.06 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 60 TYR 0.021 0.002 TYR C 36 PHE 0.019 0.003 PHE M 38 TRP 0.014 0.004 TRP P 90 HIS 0.006 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (34704) covalent geometry : angle 0.55159 / 0.31 (46728) hydrogen bonds : bond 0.05893 / 3.95 ( 2640) hydrogen bonds : angle 3.57948 / 2.58 ( 7920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 720 time to evaluate : 1.031 Fit side-chains REVERT: D 91 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8104 (mm-30) REVERT: I 91 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8109 (mm-30) REVERT: J 89 ASP cc_start: 0.7903 (t70) cc_final: 0.7550 (t70) REVERT: J 91 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8104 (mm-30) REVERT: N 91 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8109 (mm-30) REVERT: O 91 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8114 (mm-30) REVERT: Q 89 ASP cc_start: 0.7906 (t70) cc_final: 0.7529 (t70) REVERT: Q 91 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8103 (mm-30) REVERT: W 89 ASP cc_start: 0.7908 (t70) cc_final: 0.7543 (t70) REVERT: W 91 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8107 (mm-30) outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 0.8826 time to fit residues: 732.9506 Evaluate side-chains 696 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 216 optimal weight: 7.9990 chunk 301 optimal weight: 7.9990 chunk 170 optimal weight: 0.1980 chunk 362 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 323 optimal weight: 2.9990 chunk 373 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 354 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 80 GLN B 57 HIS B 72 GLN B 80 GLN C 72 GLN C 80 GLN D 72 GLN D 80 GLN E 72 GLN E 80 GLN F 57 HIS F 72 GLN F 80 GLN G 72 GLN G 80 GLN H 72 GLN H 80 GLN I 72 GLN I 80 GLN J 72 GLN J 80 GLN K 72 GLN K 80 GLN L 72 GLN L 80 GLN M 72 GLN M 80 GLN N 72 GLN N 80 GLN O 72 GLN O 80 GLN P 57 HIS P 72 GLN P 80 GLN Q 57 HIS Q 72 GLN Q 80 GLN R 72 GLN R 80 GLN S 57 HIS S 72 GLN S 80 GLN T 72 GLN T 80 GLN V 72 GLN V 80 GLN W 72 GLN W 80 GLN X 72 GLN X 80 GLN Y 57 HIS Y 72 GLN Y 80 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124800 restraints weight = 24452.563| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 0.68 r_work: 0.3185 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.2806 rms_B_bonded: 4.58 restraints_weight: 0.1250 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34704 Z= 0.163 Angle : 0.566 6.704 46728 Z= 0.318 Chirality : 0.038 0.136 4920 Planarity : 0.004 0.027 6144 Dihedral : 4.202 18.983 4512 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.65 % Allowed : 5.84 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.04 (0.13), residues: 4104 helix: 3.84 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.05 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 60 TYR 0.021 0.002 TYR B 36 PHE 0.019 0.003 PHE A 38 TRP 0.014 0.004 TRP L 90 HIS 0.007 0.002 HIS D 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (34704) covalent geometry : angle 0.56578 / 0.32 (46728) hydrogen bonds : bond 0.06062 / 4.07 ( 2640) hydrogen bonds : angle 3.61874 / 2.61 ( 7920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 702 time to evaluate : 1.392 Fit side-chains REVERT: D 91 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8052 (mm-30) REVERT: I 91 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8050 (mm-30) REVERT: J 91 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8072 (mm-30) REVERT: N 91 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8054 (mm-30) REVERT: O 91 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8057 (mm-30) REVERT: Q 91 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8069 (mm-30) REVERT: W 91 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8079 (mm-30) outliers start: 24 outliers final: 0 residues processed: 702 average time/residue: 0.8851 time to fit residues: 715.9256 Evaluate side-chains 699 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 699 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 133 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 355 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 320 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 80 GLN B 72 GLN B 80 GLN C 72 GLN C 80 GLN D 72 GLN D 80 GLN E 72 GLN E 80 GLN F 72 GLN F 80 GLN G 72 GLN G 80 GLN H 72 GLN H 80 GLN I 72 GLN I 80 GLN J 72 GLN J 80 GLN K 72 GLN K 80 GLN L 72 GLN L 80 GLN M 72 GLN M 80 GLN N 72 GLN N 80 GLN O 72 GLN O 80 GLN P 72 GLN P 80 GLN Q 72 GLN Q 80 GLN R 72 GLN R 80 GLN S 72 GLN S 80 GLN T 72 GLN T 80 GLN V 72 GLN V 80 GLN W 72 GLN W 80 GLN X 72 GLN X 80 GLN Y 72 GLN Y 80 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124202 restraints weight = 24042.666| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 0.65 r_work: 0.3209 rms_B_bonded: 0.98 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.2837 rms_B_bonded: 4.55 restraints_weight: 0.1250 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34704 Z= 0.172 Angle : 0.578 6.760 46728 Z= 0.325 Chirality : 0.039 0.137 4920 Planarity : 0.004 0.028 6144 Dihedral : 4.229 18.700 4512 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.97 (0.13), residues: 4104 helix: 3.80 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.99 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 60 TYR 0.021 0.002 TYR B 36 PHE 0.020 0.003 PHE L 38 TRP 0.014 0.004 TRP W 90 HIS 0.007 0.002 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (34704) covalent geometry : angle 0.57758 / 0.33 (46728) hydrogen bonds : bond 0.06174 / 4.14 ( 2640) hydrogen bonds : angle 3.64716 / 2.63 ( 7920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 712 time to evaluate : 1.450 Fit side-chains REVERT: D 91 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8113 (mm-30) REVERT: I 91 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8109 (mm-30) REVERT: O 91 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8125 (mm-30) REVERT: W 91 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8113 (mm-30) outliers start: 0 outliers final: 0 residues processed: 712 average time/residue: 0.8987 time to fit residues: 736.4930 Evaluate side-chains 697 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 697 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 95 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 245 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 354 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 387 optimal weight: 20.0000 chunk 311 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 80 GLN B 72 GLN B 80 GLN C 72 GLN C 80 GLN D 72 GLN D 80 GLN E 72 GLN E 80 GLN F 72 GLN F 80 GLN G 72 GLN G 80 GLN H 72 GLN H 80 GLN I 72 GLN I 80 GLN J 72 GLN J 80 GLN K 72 GLN K 80 GLN L 72 GLN L 80 GLN M 72 GLN M 80 GLN N 72 GLN N 80 GLN O 72 GLN O 80 GLN P 72 GLN P 80 GLN Q 72 GLN Q 80 GLN R 72 GLN R 80 GLN S 72 GLN S 80 GLN T 72 GLN T 80 GLN V 72 GLN V 80 GLN W 72 GLN W 80 GLN X 72 GLN X 80 GLN Y 72 GLN Y 80 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.134458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.124366 restraints weight = 24067.541| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 0.52 r_work: 0.3206 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work: 0.2822 rms_B_bonded: 4.15 restraints_weight: 0.1250 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34704 Z= 0.136 Angle : 0.526 6.318 46728 Z= 0.296 Chirality : 0.037 0.135 4920 Planarity : 0.004 0.041 6144 Dihedral : 4.139 19.483 4512 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.21 (0.13), residues: 4104 helix: 3.97 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 60 TYR 0.020 0.002 TYR A 36 PHE 0.017 0.002 PHE S 38 TRP 0.013 0.003 TRP W 90 HIS 0.006 0.001 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (34704) covalent geometry : angle 0.52620 / 0.30 (46728) hydrogen bonds : bond 0.05601 / 3.76 ( 2640) hydrogen bonds : angle 3.51794 / 2.53 ( 7920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 704 time to evaluate : 1.434 Fit side-chains REVERT: J 89 ASP cc_start: 0.7796 (t70) cc_final: 0.7589 (t70) REVERT: Q 89 ASP cc_start: 0.7803 (t70) cc_final: 0.7599 (t70) REVERT: W 89 ASP cc_start: 0.7890 (t70) cc_final: 0.7589 (t70) outliers start: 0 outliers final: 0 residues processed: 704 average time/residue: 0.8856 time to fit residues: 718.3523 Evaluate side-chains 696 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 279 optimal weight: 0.8980 chunk 260 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 347 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 80 GLN B 57 HIS B 72 GLN B 80 GLN C 72 GLN C 80 GLN D 72 GLN D 80 GLN E 72 GLN E 80 GLN F 57 HIS F 72 GLN F 80 GLN G 72 GLN G 80 GLN H 72 GLN H 80 GLN I 72 GLN I 80 GLN J 72 GLN J 80 GLN K 72 GLN K 80 GLN L 72 GLN L 80 GLN M 72 GLN M 80 GLN N 72 GLN N 80 GLN O 72 GLN O 80 GLN P 57 HIS P 72 GLN P 80 GLN Q 57 HIS Q 72 GLN Q 80 GLN R 72 GLN R 80 GLN S 57 HIS S 72 GLN S 80 GLN T 72 GLN T 80 GLN V 72 GLN V 80 GLN W 72 GLN W 80 GLN X 72 GLN X 80 GLN Y 57 HIS Y 72 GLN Y 80 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.137496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124774 restraints weight = 24584.113| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.68 r_work: 0.3197 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.2818 rms_B_bonded: 4.57 restraints_weight: 0.1250 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34704 Z= 0.151 Angle : 0.552 6.716 46728 Z= 0.310 Chirality : 0.038 0.133 4920 Planarity : 0.004 0.043 6144 Dihedral : 4.170 18.703 4512 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.65 % Allowed : 5.33 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.11 (0.13), residues: 4104 helix: 3.89 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.08 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 60 TYR 0.020 0.002 TYR B 36 PHE 0.018 0.003 PHE B 38 TRP 0.013 0.003 TRP J 90 HIS 0.007 0.002 HIS S 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (34704) covalent geometry : angle 0.55157 / 0.31 (46728) hydrogen bonds : bond 0.05895 / 3.96 ( 2640) hydrogen bonds : angle 3.57753 / 2.58 ( 7920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 691 time to evaluate : 1.396 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 691 average time/residue: 0.8679 time to fit residues: 690.8661 Evaluate side-chains 691 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 691 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 258 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 381 optimal weight: 0.9980 chunk 406 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 80 GLN B 57 HIS B 72 GLN B 80 GLN C 72 GLN C 80 GLN D 72 GLN D 80 GLN E 72 GLN E 80 GLN F 57 HIS F 72 GLN F 80 GLN G 72 GLN G 80 GLN H 72 GLN H 80 GLN I 72 GLN I 80 GLN J 72 GLN J 80 GLN K 72 GLN K 80 GLN L 72 GLN L 80 GLN M 72 GLN M 80 GLN N 72 GLN N 80 GLN O 72 GLN O 80 GLN P 72 GLN P 80 GLN Q 57 HIS Q 72 GLN Q 80 GLN R 72 GLN R 80 GLN S 57 HIS S 72 GLN S 80 GLN T 72 GLN T 80 GLN V 72 GLN V 80 GLN W 72 GLN W 80 GLN X 72 GLN X 80 GLN Y 72 GLN Y 80 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.124403 restraints weight = 24236.823| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 0.64 r_work: 0.3210 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 1.66 restraints_weight: 0.2500 r_work: 0.2829 rms_B_bonded: 4.37 restraints_weight: 0.1250 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34704 Z= 0.146 Angle : 0.543 6.788 46728 Z= 0.306 Chirality : 0.038 0.135 4920 Planarity : 0.004 0.041 6144 Dihedral : 4.147 18.598 4512 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.18 (0.13), residues: 4104 helix: 3.94 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 60 TYR 0.020 0.002 TYR B 36 PHE 0.018 0.003 PHE B 38 TRP 0.013 0.003 TRP M 90 HIS 0.007 0.002 HIS P 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (34704) covalent geometry : angle 0.54348 / 0.31 (46728) hydrogen bonds : bond 0.05766 / 3.87 ( 2640) hydrogen bonds : angle 3.54756 / 2.56 ( 7920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 697 time to evaluate : 1.462 Fit side-chains REVERT: D 89 ASP cc_start: 0.7870 (t70) cc_final: 0.7658 (t70) REVERT: G 89 ASP cc_start: 0.7756 (t70) cc_final: 0.7537 (t70) REVERT: I 89 ASP cc_start: 0.7873 (t70) cc_final: 0.7670 (t70) REVERT: O 89 ASP cc_start: 0.7841 (t70) cc_final: 0.7625 (t70) REVERT: V 89 ASP cc_start: 0.7730 (t70) cc_final: 0.7508 (t70) outliers start: 0 outliers final: 0 residues processed: 697 average time/residue: 0.9484 time to fit residues: 760.8745 Evaluate side-chains 692 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 692 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 12 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 375 optimal weight: 8.9990 chunk 136 optimal weight: 40.0000 chunk 356 optimal weight: 9.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 80 GLN B 57 HIS B 72 GLN B 80 GLN C 72 GLN C 80 GLN D 72 GLN D 80 GLN E 72 GLN E 80 GLN F 57 HIS F 72 GLN F 80 GLN F 109 GLN G 72 GLN G 80 GLN H 72 GLN H 80 GLN H 109 GLN I 72 GLN I 80 GLN J 72 GLN J 80 GLN K 72 GLN K 80 GLN L 72 GLN L 80 GLN M 72 GLN M 80 GLN N 72 GLN N 80 GLN O 72 GLN O 80 GLN P 72 GLN P 80 GLN Q 57 HIS Q 72 GLN Q 80 GLN R 72 GLN R 80 GLN S 72 GLN S 80 GLN T 72 GLN T 80 GLN V 72 GLN V 80 GLN V 109 GLN W 72 GLN W 80 GLN X 72 GLN X 80 GLN Y 72 GLN Y 80 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.122714 restraints weight = 24528.599| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 0.64 r_work: 0.3186 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 1.65 restraints_weight: 0.2500 r_work: 0.2806 rms_B_bonded: 4.35 restraints_weight: 0.1250 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 34704 Z= 0.188 Angle : 0.605 7.049 46728 Z= 0.341 Chirality : 0.040 0.136 4920 Planarity : 0.005 0.053 6144 Dihedral : 4.245 17.951 4512 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.88 (0.13), residues: 4104 helix: 3.74 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.94 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 60 TYR 0.021 0.003 TYR B 36 PHE 0.020 0.004 PHE J 38 TRP 0.015 0.004 TRP B 90 HIS 0.008 0.002 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (34704) covalent geometry : angle 0.60534 / 0.34 (46728) hydrogen bonds : bond 0.06365 / 4.27 ( 2640) hydrogen bonds : angle 3.69385 / 2.67 ( 7920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 1.462 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 695 average time/residue: 0.9016 time to fit residues: 720.9915 Evaluate side-chains 695 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 398 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 402 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 271 optimal weight: 30.0000 chunk 342 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 80 GLN B 57 HIS B 72 GLN B 80 GLN C 72 GLN C 80 GLN D 72 GLN D 80 GLN E 72 GLN E 80 GLN F 72 GLN F 80 GLN G 72 GLN G 80 GLN H 72 GLN H 80 GLN I 72 GLN I 80 GLN J 72 GLN J 80 GLN K 72 GLN K 80 GLN L 72 GLN L 80 GLN M 72 GLN M 80 GLN N 72 GLN N 80 GLN O 72 GLN O 80 GLN P 72 GLN P 80 GLN Q 72 GLN Q 80 GLN R 72 GLN R 80 GLN S 72 GLN S 80 GLN T 72 GLN T 80 GLN V 72 GLN V 80 GLN W 72 GLN W 80 GLN X 72 GLN X 80 GLN Y 72 GLN Y 80 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123262 restraints weight = 24324.729| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 0.64 r_work: 0.3197 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 1.65 restraints_weight: 0.2500 r_work: 0.2818 rms_B_bonded: 4.35 restraints_weight: 0.1250 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34704 Z= 0.171 Angle : 0.582 6.908 46728 Z= 0.328 Chirality : 0.039 0.136 4920 Planarity : 0.005 0.048 6144 Dihedral : 4.223 18.122 4512 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.65 % Allowed : 6.25 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.91 (0.13), residues: 4104 helix: 3.77 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.91 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 60 TYR 0.022 0.002 TYR C 36 PHE 0.019 0.003 PHE S 38 TRP 0.013 0.004 TRP B 90 HIS 0.007 0.002 HIS S 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (34704) covalent geometry : angle 0.58183 / 0.33 (46728) hydrogen bonds : bond 0.06116 / 4.10 ( 2640) hydrogen bonds : angle 3.64736 / 2.63 ( 7920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20903.32 seconds wall clock time: 354 minutes 52.20 seconds (21292.20 seconds total)