Starting phenix.real_space_refine on Fri Mar 6 21:30:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjr_54951/03_2026/9sjr_54951_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjr_54951/03_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_54951/03_2026/9sjr_54951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjr_54951/03_2026/9sjr_54951.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjr_54951/03_2026/9sjr_54951_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjr_54951/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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, 5 Unusual residues: {' FE': 4, ' MG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 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: 3.38, per 1000 atoms: 0.10 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 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: 0.75 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: 6.52 Time building geometry restraints manager: 4.01 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 1.480 nonbonded pdb="FE FE R 204 " pdb="FE FE R 205 " model vdw 0.004 1.480 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: 0.10 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: 2.740 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.660 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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:8.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 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 covalent geometry : bond 0.00258 (34704) covalent geometry : angle 0.54121 (46728) hydrogen bonds : bond 0.08196 ( 2640) hydrogen bonds : angle 3.92093 ( 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 : 1.111 Fit side-chains outliers start: 48 outliers final: 24 residues processed: 744 average time/residue: 0.9019 time to fit residues: 767.3681 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 : 1.294 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3544 r_free = 0.3544 target = 0.140588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127999 restraints weight = 24692.806| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 0.67 r_work: 0.3268 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work: 0.2898 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 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 = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.0839 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 : 0.472 5.553 46728 Z= 0.261 Chirality : 0.035 0.124 4920 Planarity : 0.003 0.022 6144 Dihedral : 4.086 19.395 4536 Min Nonbonded Distance : 1.019 Molprobity Statistics. All-atom Clashscore : 3.08 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: 5.52 (0.13), residues: 4104 helix: 4.19 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.15 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 60 TYR 0.017 0.002 TYR F 36 PHE 0.015 0.002 PHE T 38 TRP 0.009 0.002 TRP P 90 HIS 0.006 0.001 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00197 (34704) covalent geometry : angle 0.47165 (46728) hydrogen bonds : bond 0.04711 ( 2640) hydrogen bonds : angle 3.37349 ( 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 : 1.293 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 717 average time/residue: 0.9166 time to fit residues: 750.2149 Evaluate side-chains 687 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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: 9.9990 chunk 162 optimal weight: 0.8980 chunk 192 optimal weight: 20.0000 chunk 391 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 167 optimal weight: 1.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B 80 GLN C 80 GLN D 80 GLN E 80 GLN F 80 GLN G 80 GLN H 80 GLN I 80 GLN J 80 GLN K 80 GLN L 80 GLN M 80 GLN N 80 GLN O 80 GLN P 80 GLN Q 80 GLN R 80 GLN S 80 GLN T 80 GLN V 80 GLN W 80 GLN X 80 GLN Y 80 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.124886 restraints weight = 24452.834| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 0.63 r_work: 0.3218 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 1.60 restraints_weight: 0.2500 r_work: 0.2839 rms_B_bonded: 4.25 restraints_weight: 0.1250 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 34704 Z= 0.136 Angle : 0.522 6.293 46728 Z= 0.292 Chirality : 0.037 0.130 4920 Planarity : 0.003 0.026 6144 Dihedral : 4.076 19.817 4512 Min Nonbonded Distance : 1.017 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.19 % Allowed : 4.98 % Favored : 93.83 % 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: 5.32 (0.13), residues: 4104 helix: 4.04 (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 0.006 0.001 ARG L 60 TYR 0.020 0.002 TYR F 36 PHE 0.017 0.002 PHE C 38 TRP 0.013 0.003 TRP V 90 HIS 0.006 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00249 (34704) covalent geometry : angle 0.52178 (46728) hydrogen bonds : bond 0.05599 ( 2640) hydrogen bonds : angle 3.50016 ( 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 754 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 710 time to evaluate : 1.301 Fit side-chains outliers start: 44 outliers final: 0 residues processed: 730 average time/residue: 0.9363 time to fit residues: 779.1568 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 : 1.247 ------------------------------------------------------------------------------- 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: 9.9990 chunk 176 optimal weight: 20.0000 chunk 405 optimal weight: 5.9990 chunk 367 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 317 optimal weight: 20.0000 chunk 271 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B 80 GLN C 80 GLN D 80 GLN E 80 GLN F 80 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 72 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.123358 restraints weight = 24385.467| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 0.62 r_work: 0.3208 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.2826 rms_B_bonded: 4.31 restraints_weight: 0.1250 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.0710 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= 0.172 Angle : 0.580 6.666 46728 Z= 0.326 Chirality : 0.039 0.134 4920 Planarity : 0.004 0.032 6144 Dihedral : 4.202 18.590 4512 Min Nonbonded Distance : 0.952 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % 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: 3.87 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.14 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 60 TYR 0.021 0.003 TYR S 36 PHE 0.020 0.003 PHE G 38 TRP 0.013 0.004 TRP R 90 HIS 0.006 0.002 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00332 (34704) covalent geometry : angle 0.57994 (46728) hydrogen bonds : bond 0.06170 ( 2640) hydrogen bonds : angle 3.63623 ( 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 702 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 702 time to evaluate : 1.015 Fit side-chains REVERT: A 89 ASP cc_start: 0.7871 (t70) cc_final: 0.7534 (t70) REVERT: A 91 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8061 (mm-30) REVERT: B 89 ASP cc_start: 0.7878 (t70) cc_final: 0.7541 (t70) REVERT: B 91 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8066 (mm-30) REVERT: C 89 ASP cc_start: 0.7881 (t70) cc_final: 0.7544 (t70) REVERT: C 91 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8057 (mm-30) REVERT: D 89 ASP cc_start: 0.7875 (t70) cc_final: 0.7533 (t70) REVERT: D 91 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8084 (mm-30) REVERT: H 89 ASP cc_start: 0.7888 (t70) cc_final: 0.7551 (t70) REVERT: H 91 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8061 (mm-30) REVERT: I 89 ASP cc_start: 0.7867 (t70) cc_final: 0.7547 (t70) REVERT: I 91 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8077 (mm-30) REVERT: J 89 ASP cc_start: 0.7867 (t70) cc_final: 0.7542 (t70) REVERT: J 91 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8078 (mm-30) REVERT: M 89 ASP cc_start: 0.7881 (t70) cc_final: 0.7530 (t70) REVERT: M 91 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8064 (mm-30) REVERT: N 89 ASP cc_start: 0.7874 (t70) cc_final: 0.7530 (t70) REVERT: N 91 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8083 (mm-30) REVERT: O 89 ASP cc_start: 0.7868 (t70) cc_final: 0.7544 (t70) REVERT: O 91 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8073 (mm-30) REVERT: Q 89 ASP cc_start: 0.7880 (t70) cc_final: 0.7548 (t70) REVERT: Q 91 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8064 (mm-30) REVERT: W 89 ASP cc_start: 0.7880 (t70) cc_final: 0.7555 (t70) REVERT: W 91 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8076 (mm-30) outliers start: 0 outliers final: 0 residues processed: 702 average time/residue: 0.8940 time to fit residues: 718.4836 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 : 1.253 ------------------------------------------------------------------------------- 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: 6.9990 chunk 170 optimal weight: 0.0070 chunk 362 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 323 optimal weight: 0.0770 chunk 373 optimal weight: 30.0000 chunk 293 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 354 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 overall best weight: 2.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 57 HIS 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: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125803 restraints weight = 24460.068| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 0.65 r_work: 0.3238 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.2859 rms_B_bonded: 4.50 restraints_weight: 0.1250 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 34704 Z= 0.122 Angle : 0.491 6.052 46728 Z= 0.276 Chirality : 0.036 0.129 4920 Planarity : 0.003 0.019 6144 Dihedral : 4.069 19.611 4512 Min Nonbonded Distance : 1.026 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.65 % Allowed : 6.17 % Favored : 93.18 % 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: 5.40 (0.13), residues: 4104 helix: 4.10 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.12 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 60 TYR 0.018 0.002 TYR V 36 PHE 0.016 0.002 PHE L 38 TRP 0.011 0.003 TRP L 90 HIS 0.007 0.001 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00216 (34704) covalent geometry : angle 0.49070 (46728) hydrogen bonds : bond 0.05237 ( 2640) hydrogen bonds : angle 3.42883 ( 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 733 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 709 time to evaluate : 1.264 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 709 average time/residue: 0.8991 time to fit residues: 729.8363 Evaluate side-chains 685 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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: 9.9990 chunk 355 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 290 optimal weight: 8.9990 chunk 233 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 237 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B 57 HIS B 80 GLN C 80 GLN D 72 GLN D 80 GLN E 72 GLN E 80 GLN F 80 GLN G 80 GLN H 80 GLN I 80 GLN J 72 GLN J 80 GLN K 80 GLN L 72 GLN L 80 GLN M 80 GLN N 72 GLN N 80 GLN O 72 GLN O 80 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 80 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.121847 restraints weight = 24456.729| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 0.65 r_work: 0.3194 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work: 0.2820 rms_B_bonded: 4.45 restraints_weight: 0.1250 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 34704 Z= 0.220 Angle : 0.641 6.992 46728 Z= 0.361 Chirality : 0.042 0.135 4920 Planarity : 0.005 0.040 6144 Dihedral : 4.284 18.552 4512 Min Nonbonded Distance : 0.907 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.08 % Allowed : 6.79 % Favored : 93.13 % 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: 4.80 (0.13), residues: 4104 helix: 3.67 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.96 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 60 TYR 0.023 0.003 TYR J 36 PHE 0.022 0.004 PHE G 38 TRP 0.015 0.005 TRP Y 90 HIS 0.008 0.002 HIS Y 57 Details of bonding type rmsd covalent geometry : bond 0.00438 (34704) covalent geometry : angle 0.64054 (46728) hydrogen bonds : bond 0.06649 ( 2640) hydrogen bonds : angle 3.75602 ( 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 675 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 672 time to evaluate : 1.370 Fit side-chains REVERT: A 89 ASP cc_start: 0.7929 (t70) cc_final: 0.7577 (t70) REVERT: B 89 ASP cc_start: 0.7930 (t70) cc_final: 0.7573 (t70) REVERT: C 89 ASP cc_start: 0.7941 (t70) cc_final: 0.7587 (t70) REVERT: D 89 ASP cc_start: 0.7935 (t70) cc_final: 0.7636 (t70) REVERT: D 91 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8167 (mm-30) REVERT: H 89 ASP cc_start: 0.7945 (t70) cc_final: 0.7601 (t70) REVERT: H 91 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8172 (mm-30) REVERT: I 89 ASP cc_start: 0.7941 (t70) cc_final: 0.7642 (t70) REVERT: I 91 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8175 (mm-30) REVERT: J 89 ASP cc_start: 0.7940 (t70) cc_final: 0.7638 (t70) REVERT: J 91 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8166 (mm-30) REVERT: K 89 ASP cc_start: 0.7955 (t70) cc_final: 0.7619 (t70) REVERT: M 89 ASP cc_start: 0.7942 (t70) cc_final: 0.7634 (t70) REVERT: N 89 ASP cc_start: 0.7944 (t70) cc_final: 0.7648 (t70) REVERT: N 91 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8172 (mm-30) REVERT: O 89 ASP cc_start: 0.7939 (t70) cc_final: 0.7641 (t70) REVERT: O 91 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8160 (mm-30) REVERT: Q 89 ASP cc_start: 0.7931 (t70) cc_final: 0.7579 (t70) REVERT: Q 91 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8159 (mm-30) REVERT: S 89 ASP cc_start: 0.7953 (t70) cc_final: 0.7589 (t70) REVERT: S 91 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8177 (mm-30) REVERT: W 89 ASP cc_start: 0.7937 (t70) cc_final: 0.7634 (t70) REVERT: W 91 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8174 (mm-30) outliers start: 3 outliers final: 0 residues processed: 672 average time/residue: 0.9219 time to fit residues: 707.0880 Evaluate side-chains 672 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 354 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 387 optimal weight: 20.0000 chunk 311 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3478 r_free = 0.3478 target = 0.135859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.123790 restraints weight = 24453.411| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.62 r_work: 0.3228 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.2850 rms_B_bonded: 4.35 restraints_weight: 0.1250 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 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 0.024 34704 Z= 0.155 Angle : 0.562 6.743 46728 Z= 0.316 Chirality : 0.038 0.137 4920 Planarity : 0.004 0.029 6144 Dihedral : 4.198 18.597 4512 Min Nonbonded Distance : 0.974 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % 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: 5.03 (0.13), residues: 4104 helix: 3.84 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.01 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 60 TYR 0.021 0.002 TYR K 36 PHE 0.019 0.003 PHE K 38 TRP 0.014 0.004 TRP V 90 HIS 0.008 0.002 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00293 (34704) covalent geometry : angle 0.56163 (46728) hydrogen bonds : bond 0.05928 ( 2640) hydrogen bonds : angle 3.59457 ( 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 706 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 706 time to evaluate : 1.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 706 average time/residue: 0.9117 time to fit residues: 734.5940 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 : 1.219 ------------------------------------------------------------------------------- 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: 1.9990 chunk 260 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3468 r_free = 0.3468 target = 0.135086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123058 restraints weight = 24467.297| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 0.62 r_work: 0.3217 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 1.61 restraints_weight: 0.2500 r_work: 0.2839 rms_B_bonded: 4.31 restraints_weight: 0.1250 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.0775 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= 0.179 Angle : 0.596 7.003 46728 Z= 0.335 Chirality : 0.039 0.137 4920 Planarity : 0.004 0.033 6144 Dihedral : 4.247 18.098 4512 Min Nonbonded Distance : 0.941 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.65 % Allowed : 6.41 % Favored : 92.94 % 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: 4.86 (0.13), residues: 4104 helix: 3.72 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.96 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG T 60 TYR 0.022 0.003 TYR K 36 PHE 0.020 0.003 PHE Y 38 TRP 0.013 0.004 TRP I 90 HIS 0.009 0.002 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00345 (34704) covalent geometry : angle 0.59649 (46728) hydrogen bonds : bond 0.06263 ( 2640) hydrogen bonds : angle 3.67169 ( 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 721 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 697 time to evaluate : 1.443 Fit side-chains REVERT: D 89 ASP cc_start: 0.7895 (t0) cc_final: 0.7581 (t70) REVERT: D 91 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8105 (mm-30) REVERT: I 89 ASP cc_start: 0.7890 (t0) cc_final: 0.7576 (t70) REVERT: I 91 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8103 (mm-30) REVERT: J 89 ASP cc_start: 0.7889 (t0) cc_final: 0.7573 (t70) REVERT: J 91 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8095 (mm-30) REVERT: N 89 ASP cc_start: 0.7903 (t0) cc_final: 0.7588 (t70) REVERT: N 91 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8111 (mm-30) REVERT: O 89 ASP cc_start: 0.7901 (t0) cc_final: 0.7584 (t70) REVERT: O 91 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8100 (mm-30) REVERT: W 89 ASP cc_start: 0.7891 (t0) cc_final: 0.7574 (t70) REVERT: W 91 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8106 (mm-30) outliers start: 24 outliers final: 0 residues processed: 697 average time/residue: 0.9044 time to fit residues: 721.2853 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 : 1.095 ------------------------------------------------------------------------------- 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: 7.9990 chunk 201 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 381 optimal weight: 0.8980 chunk 406 optimal weight: 6.9990 chunk 156 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3541 r_free = 0.3541 target = 0.140747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.128414 restraints weight = 24535.344| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 0.65 r_work: 0.3269 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.2888 rms_B_bonded: 4.55 restraints_weight: 0.1250 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 34704 Z= 0.108 Angle : 0.460 5.642 46728 Z= 0.259 Chirality : 0.035 0.130 4920 Planarity : 0.002 0.018 6144 Dihedral : 3.991 19.320 4512 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % 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: 5.60 (0.13), residues: 4104 helix: 4.26 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.12 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 60 TYR 0.016 0.002 TYR K 36 PHE 0.014 0.002 PHE A 38 TRP 0.012 0.003 TRP L 90 HIS 0.008 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00185 (34704) covalent geometry : angle 0.46040 (46728) hydrogen bonds : bond 0.04575 ( 2640) hydrogen bonds : angle 3.31418 ( 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 705 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 705 time to evaluate : 1.423 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 705 average time/residue: 0.9260 time to fit residues: 743.2356 Evaluate side-chains 682 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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: 6.9990 chunk 46 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 375 optimal weight: 7.9990 chunk 136 optimal weight: 40.0000 chunk 356 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B 20 GLN B 57 HIS B 80 GLN C 80 GLN D 80 GLN E 80 GLN F 57 HIS F 80 GLN G 80 GLN H 80 GLN I 80 GLN J 80 GLN K 80 GLN L 80 GLN M 80 GLN N 80 GLN O 80 GLN P 57 HIS P 80 GLN Q 57 HIS Q 80 GLN R 80 GLN S 57 HIS S 80 GLN T 80 GLN V 80 GLN W 80 GLN X 80 GLN Y 57 HIS Y 80 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.122751 restraints weight = 24562.686| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 0.65 r_work: 0.3185 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.2799 rms_B_bonded: 4.49 restraints_weight: 0.1250 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 34704 Z= 0.185 Angle : 0.601 6.908 46728 Z= 0.339 Chirality : 0.040 0.133 4920 Planarity : 0.004 0.035 6144 Dihedral : 4.210 18.273 4512 Min Nonbonded Distance : 0.944 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % 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: 5.01 (0.13), residues: 4104 helix: 3.83 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.03 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 60 TYR 0.022 0.003 TYR C 36 PHE 0.021 0.003 PHE C 38 TRP 0.015 0.004 TRP B 90 HIS 0.008 0.002 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00362 (34704) covalent geometry : angle 0.60092 (46728) hydrogen bonds : bond 0.06290 ( 2640) hydrogen bonds : angle 3.65722 ( 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 688 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 1.336 Fit side-chains REVERT: D 91 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8025 (mm-30) REVERT: H 91 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8039 (mm-30) REVERT: I 91 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8025 (mm-30) REVERT: J 91 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8020 (mm-30) REVERT: N 91 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8029 (mm-30) REVERT: O 91 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8022 (mm-30) REVERT: Q 91 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8040 (mm-30) REVERT: S 91 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8071 (mm-30) REVERT: W 91 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8032 (mm-30) outliers start: 0 outliers final: 0 residues processed: 688 average time/residue: 0.8968 time to fit residues: 706.2333 Evaluate side-chains 688 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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: 0.6980 chunk 20 optimal weight: 8.9990 chunk 402 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 118 optimal weight: 30.0000 chunk 271 optimal weight: 30.0000 chunk 342 optimal weight: 9.9990 chunk 286 optimal weight: 5.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3474 r_free = 0.3474 target = 0.135485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.122987 restraints weight = 24379.718| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.64 r_work: 0.3190 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work: 0.2804 rms_B_bonded: 4.47 restraints_weight: 0.1250 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34704 Z= 0.178 Angle : 0.593 6.812 46728 Z= 0.334 Chirality : 0.039 0.136 4920 Planarity : 0.004 0.037 6144 Dihedral : 4.233 18.379 4512 Min Nonbonded Distance : 0.946 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.65 % Allowed : 7.55 % Favored : 91.80 % 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: 4.88 (0.13), residues: 4104 helix: 3.74 (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 0.007 0.001 ARG R 60 TYR 0.022 0.003 TYR N 36 PHE 0.020 0.003 PHE C 38 TRP 0.016 0.004 TRP S 90 HIS 0.008 0.002 HIS T 57 Details of bonding type rmsd covalent geometry : bond 0.00345 (34704) covalent geometry : angle 0.59283 (46728) hydrogen bonds : bond 0.06218 ( 2640) hydrogen bonds : angle 3.65432 ( 7920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20891.04 seconds wall clock time: 354 minutes 12.53 seconds (21252.53 seconds total)