Starting phenix.real_space_refine on Tue Aug 26 11:15:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuy_60915/08_2025/9iuy_60915.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuy_60915/08_2025/9iuy_60915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iuy_60915/08_2025/9iuy_60915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuy_60915/08_2025/9iuy_60915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iuy_60915/08_2025/9iuy_60915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuy_60915/08_2025/9iuy_60915.map" } resolution = 1.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.101 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: 7 Type Number sf(0) Gaussians K 24 8.98 5 Fe 6 7.16 5 Mg 32 5.21 5 S 192 5.16 5 C 21432 2.51 5 N 6024 2.21 5 O 9840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37550 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 1, ' FE': 1, ' MG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "B" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "C" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "D" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "E" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "F" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "G" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "H" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "I" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "J" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "K" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "L" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "M" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "N" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "O" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "P" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "Q" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "R" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "S" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "T" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "U" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "V" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "W" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "X" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 4.86, per 1000 atoms: 0.13 Number of scatterers: 37550 At special positions: 0 Unit cell: (132.84, 132.84, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 6 26.01 K 24 19.00 S 192 16.00 Mg 32 11.99 O 9840 8.00 N 6024 7.00 C 21432 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: 3.23 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.4 microseconds 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU U 167 " --> pdb=" O ALA U 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 4.305A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (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: 6.40 Time building geometry restraints manager: 4.15 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: 11640 1.34 - 1.46: 6383 1.46 - 1.58: 16585 1.58 - 1.69: 0 1.69 - 1.81: 312 Bond restraints: 34920 Sorted by residual: bond pdb=" N ASP T 89 " pdb=" CA ASP T 89 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.51e+00 bond pdb=" N ASP D 89 " pdb=" CA ASP D 89 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.51e+00 bond pdb=" N ASP F 89 " pdb=" CA ASP F 89 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.51e+00 bond pdb=" N ASP A 89 " pdb=" CA ASP A 89 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.51e+00 bond pdb=" N ASP C 89 " pdb=" CA ASP C 89 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.51e+00 ... (remaining 34915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 44398 1.23 - 2.47: 2042 2.47 - 3.70: 456 3.70 - 4.94: 48 4.94 - 6.17: 48 Bond angle restraints: 46992 Sorted by residual: angle pdb=" C TRP F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C TRP G 93 " pdb=" N GLU G 94 " pdb=" CA GLU G 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C TRP C 93 " pdb=" N GLU C 94 " pdb=" CA GLU C 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C TRP W 93 " pdb=" N GLU W 94 " pdb=" CA GLU W 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C TRP J 93 " pdb=" N GLU J 94 " pdb=" CA GLU J 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 ... (remaining 46987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 19200 15.13 - 30.25: 1512 30.25 - 45.38: 216 45.38 - 60.51: 216 60.51 - 75.63: 72 Dihedral angle restraints: 21216 sinusoidal: 8832 harmonic: 12384 Sorted by residual: dihedral pdb=" CA TRP D 93 " pdb=" C TRP D 93 " pdb=" N GLU D 94 " pdb=" CA GLU D 94 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP U 93 " pdb=" C TRP U 93 " pdb=" N GLU U 94 " pdb=" CA GLU U 94 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP H 93 " pdb=" C TRP H 93 " pdb=" N GLU H 94 " pdb=" CA GLU H 94 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 21213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3719 0.038 - 0.076: 817 0.076 - 0.114: 240 0.114 - 0.152: 96 0.152 - 0.190: 24 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CG LEU J 72 " pdb=" CB LEU J 72 " pdb=" CD1 LEU J 72 " pdb=" CD2 LEU J 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CG LEU C 72 " pdb=" CB LEU C 72 " pdb=" CD1 LEU C 72 " pdb=" CD2 LEU C 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CG LEU X 72 " pdb=" CB LEU X 72 " pdb=" CD1 LEU X 72 " pdb=" CD2 LEU X 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.03e-01 ... (remaining 4893 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 32 " -0.030 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR Q 32 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 32 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 32 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR Q 32 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR Q 32 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 32 " 0.030 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR G 32 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR G 32 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR G 32 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR G 32 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR G 32 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 32 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " 0.030 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR F 32 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " 0.005 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 2736 2.69 - 3.30: 47113 3.30 - 3.92: 93227 3.92 - 4.53: 127654 4.53 - 5.14: 177578 Nonbonded interactions: 448308 Sorted by model distance: nonbonded pdb="MG MG U 201 " pdb=" O HOH U 336 " model vdw 2.080 2.170 nonbonded pdb="MG MG L 201 " pdb=" O HOH L 336 " model vdw 2.080 2.170 nonbonded pdb="MG MG D 201 " pdb=" O HOH D 336 " model vdw 2.080 2.170 nonbonded pdb="MG MG M 201 " pdb=" O HOH M 336 " model vdw 2.080 2.170 nonbonded pdb="MG MG E 201 " pdb=" O HOH E 336 " model vdw 2.080 2.170 ... (remaining 448303 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 202) selection = (chain 'B' and resid 4 through 202) selection = (chain 'C' and resid 4 through 202) selection = (chain 'D' and resid 4 through 202) selection = (chain 'E' and resid 4 through 202) selection = chain 'F' selection = chain 'G' selection = (chain 'H' and resid 4 through 202) selection = (chain 'I' and resid 4 through 202) selection = (chain 'J' and resid 4 through 202) selection = chain 'K' selection = (chain 'L' and resid 4 through 202) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 4 through 202) selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 28.140 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.120 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34920 Z= 0.216 Angle : 0.649 6.173 46992 Z= 0.376 Chirality : 0.041 0.190 4896 Planarity : 0.005 0.034 6192 Dihedral : 13.662 75.634 13200 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.29 (0.13), residues: 4128 helix: 3.41 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.59 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 76 TYR 0.054 0.004 TYR W 32 PHE 0.019 0.004 PHE W 41 TRP 0.012 0.004 TRP K 93 HIS 0.006 0.002 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00416 (34920) covalent geometry : angle 0.64940 (46992) hydrogen bonds : bond 0.07430 ( 2640) hydrogen bonds : angle 4.17721 ( 7920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1032 time to evaluate : 1.627 Fit side-chains outliers start: 0 outliers final: 24 residues processed: 1032 average time/residue: 1.0213 time to fit residues: 1201.2997 Evaluate side-chains 960 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 936 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.177430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.164933 restraints weight = 12668.276| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 0.27 r_work: 0.3711 rms_B_bonded: 0.50 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 0.92 restraints_weight: 0.2500 r_work: 0.3264 rms_B_bonded: 2.54 restraints_weight: 0.1250 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34920 Z= 0.202 Angle : 0.648 6.380 46992 Z= 0.351 Chirality : 0.038 0.125 4896 Planarity : 0.004 0.021 6192 Dihedral : 4.752 21.707 4656 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.22 (0.13), residues: 4128 helix: 3.37 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.53 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 63 TYR 0.024 0.003 TYR L 32 PHE 0.018 0.003 PHE U 41 TRP 0.013 0.004 TRP N 93 HIS 0.006 0.002 HIS R 128 Details of bonding type rmsd covalent geometry : bond 0.00420 (34920) covalent geometry : angle 0.64752 (46992) hydrogen bonds : bond 0.05731 ( 2640) hydrogen bonds : angle 3.91706 ( 7920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 939 time to evaluate : 1.490 Fit side-chains REVERT: A 90 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7253 (mtp85) REVERT: B 90 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7259 (mtp85) REVERT: C 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7259 (mtp85) REVERT: D 90 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7256 (mtp85) REVERT: E 90 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7255 (mtp85) REVERT: F 90 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7256 (mtp85) REVERT: G 90 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7257 (mtp85) REVERT: H 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7259 (mtp85) REVERT: I 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7260 (mtp85) REVERT: J 90 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7260 (mtp85) REVERT: K 90 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7261 (mtp85) REVERT: L 90 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7258 (mtp85) REVERT: M 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7261 (mtp85) REVERT: N 90 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7261 (mtp85) REVERT: O 90 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7261 (mtp85) REVERT: P 90 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7261 (mtp85) REVERT: Q 90 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7258 (mtp85) REVERT: R 90 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7262 (mtp85) REVERT: S 90 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7262 (mtp85) REVERT: T 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7255 (mtp85) REVERT: U 90 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7256 (mtp85) REVERT: V 90 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7258 (mtp85) REVERT: W 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7258 (mtp85) REVERT: X 90 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7261 (mtp85) outliers start: 0 outliers final: 0 residues processed: 939 average time/residue: 1.0861 time to fit residues: 1155.4525 Evaluate side-chains 936 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 936 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 17 optimal weight: 20.0000 chunk 293 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 338 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 262 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 141 GLN B 25 ASN B 141 GLN C 25 ASN C 141 GLN D 25 ASN D 141 GLN E 25 ASN E 141 GLN F 25 ASN F 141 GLN G 25 ASN G 141 GLN H 25 ASN H 141 GLN I 25 ASN I 141 GLN J 25 ASN J 141 GLN K 25 ASN K 141 GLN L 25 ASN L 141 GLN M 25 ASN M 141 GLN N 25 ASN N 141 GLN O 25 ASN O 141 GLN P 25 ASN P 141 GLN Q 25 ASN Q 141 GLN R 25 ASN R 141 GLN S 25 ASN S 141 GLN T 25 ASN T 141 GLN U 25 ASN U 141 GLN V 25 ASN V 141 GLN W 25 ASN W 141 GLN X 25 ASN X 141 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.179790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.167474 restraints weight = 12792.781| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 0.27 r_work: 0.3745 rms_B_bonded: 0.49 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 0.91 restraints_weight: 0.2500 r_work: 0.3302 rms_B_bonded: 2.55 restraints_weight: 0.1250 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34920 Z= 0.139 Angle : 0.540 5.568 46992 Z= 0.291 Chirality : 0.036 0.122 4896 Planarity : 0.003 0.021 6192 Dihedral : 4.351 21.341 4560 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.57 % Allowed : 5.19 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.59 (0.13), residues: 4128 helix: 3.61 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.76 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 63 TYR 0.015 0.002 TYR I 137 PHE 0.015 0.002 PHE V 41 TRP 0.012 0.003 TRP M 93 HIS 0.004 0.001 HIS N 128 Details of bonding type rmsd covalent geometry : bond 0.00282 (34920) covalent geometry : angle 0.54014 (46992) hydrogen bonds : bond 0.04940 ( 2640) hydrogen bonds : angle 3.67512 ( 7920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 936 time to evaluate : 1.477 Fit side-chains REVERT: A 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7239 (mtp85) REVERT: A 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8043 (mmtm) REVERT: B 90 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7239 (mtp85) REVERT: B 157 LYS cc_start: 0.8299 (mttp) cc_final: 0.8040 (mmtm) REVERT: C 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7244 (mtp85) REVERT: C 157 LYS cc_start: 0.8302 (mttp) cc_final: 0.8044 (mmtm) REVERT: D 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7245 (mtp85) REVERT: D 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8042 (mmtm) REVERT: E 90 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7243 (mtp85) REVERT: E 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8043 (mmtm) REVERT: F 90 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7238 (mtp85) REVERT: F 157 LYS cc_start: 0.8302 (mttp) cc_final: 0.8043 (mmtm) REVERT: G 90 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7242 (mtp85) REVERT: G 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8043 (mmtm) REVERT: H 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7245 (mtp85) REVERT: H 157 LYS cc_start: 0.8306 (mttp) cc_final: 0.8049 (mmtm) REVERT: I 90 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7245 (mtp85) REVERT: I 157 LYS cc_start: 0.8303 (mttp) cc_final: 0.8045 (mmtm) REVERT: J 90 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7247 (mtp85) REVERT: J 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8041 (mmtm) REVERT: K 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7244 (mtp85) REVERT: K 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8043 (mmtm) REVERT: L 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7239 (mtp85) REVERT: L 157 LYS cc_start: 0.8299 (mttp) cc_final: 0.8041 (mmtm) REVERT: M 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7245 (mtp85) REVERT: M 157 LYS cc_start: 0.8305 (mttp) cc_final: 0.8046 (mmtm) REVERT: N 90 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7243 (mtp85) REVERT: N 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8043 (mmtm) REVERT: O 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7245 (mtp85) REVERT: O 157 LYS cc_start: 0.8303 (mttp) cc_final: 0.8044 (mmtm) REVERT: P 90 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7244 (mtp85) REVERT: P 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8044 (mmtm) REVERT: Q 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7240 (mtp85) REVERT: Q 157 LYS cc_start: 0.8301 (mttp) cc_final: 0.8042 (mmtm) REVERT: R 90 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7247 (mtp85) REVERT: R 157 LYS cc_start: 0.8302 (mttp) cc_final: 0.8043 (mmtm) REVERT: S 90 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7246 (mtp85) REVERT: S 157 LYS cc_start: 0.8304 (mttp) cc_final: 0.8045 (mmtm) REVERT: T 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7238 (mtp85) REVERT: T 157 LYS cc_start: 0.8298 (mttp) cc_final: 0.8041 (mmtm) REVERT: U 90 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7243 (mtp85) REVERT: U 157 LYS cc_start: 0.8301 (mttp) cc_final: 0.8043 (mmtm) REVERT: V 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7245 (mtp85) REVERT: V 157 LYS cc_start: 0.8301 (mttp) cc_final: 0.8044 (mmtm) REVERT: W 90 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7243 (mtp85) REVERT: W 157 LYS cc_start: 0.8300 (mttp) cc_final: 0.8043 (mmtm) REVERT: X 90 ARG cc_start: 0.7490 (mtt180) cc_final: 0.7248 (mtp85) REVERT: X 157 LYS cc_start: 0.8301 (mttp) cc_final: 0.8043 (mmtm) outliers start: 21 outliers final: 21 residues processed: 936 average time/residue: 1.1450 time to fit residues: 1211.9792 Evaluate side-chains 931 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 910 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 82 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 225 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.178422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.166191 restraints weight = 12747.648| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 0.27 r_work: 0.3730 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 0.90 restraints_weight: 0.2500 r_work: 0.3290 rms_B_bonded: 2.51 restraints_weight: 0.1250 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34920 Z= 0.149 Angle : 0.566 5.255 46992 Z= 0.306 Chirality : 0.036 0.122 4896 Planarity : 0.003 0.022 6192 Dihedral : 4.447 23.170 4560 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.30 % Allowed : 6.06 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.59 (0.13), residues: 4128 helix: 3.65 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.69 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 156 TYR 0.015 0.002 TYR W 137 PHE 0.016 0.003 PHE Q 41 TRP 0.013 0.003 TRP Q 93 HIS 0.005 0.001 HIS H 128 Details of bonding type rmsd covalent geometry : bond 0.00304 (34920) covalent geometry : angle 0.56555 (46992) hydrogen bonds : bond 0.05125 ( 2640) hydrogen bonds : angle 3.74013 ( 7920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 888 time to evaluate : 1.667 Fit side-chains REVERT: A 90 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7220 (mtp85) REVERT: A 157 LYS cc_start: 0.8317 (mttp) cc_final: 0.8054 (mmtm) REVERT: A 158 MET cc_start: 0.8920 (mtp) cc_final: 0.8629 (mtp) REVERT: B 90 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7215 (mtp85) REVERT: B 157 LYS cc_start: 0.8315 (mttp) cc_final: 0.8049 (mmtm) REVERT: C 90 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7219 (mtp85) REVERT: C 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8057 (mmtm) REVERT: D 90 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7217 (mtp85) REVERT: D 157 LYS cc_start: 0.8317 (mttp) cc_final: 0.8056 (mmtm) REVERT: D 158 MET cc_start: 0.8920 (mtp) cc_final: 0.8657 (mtp) REVERT: E 90 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7218 (mtp85) REVERT: E 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8057 (mmtm) REVERT: E 158 MET cc_start: 0.8922 (mtp) cc_final: 0.8632 (mtp) REVERT: F 90 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7218 (mtp85) REVERT: F 157 LYS cc_start: 0.8316 (mttp) cc_final: 0.8053 (mmtm) REVERT: F 158 MET cc_start: 0.8919 (mtp) cc_final: 0.8626 (mtp) REVERT: G 90 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7214 (mtp85) REVERT: G 157 LYS cc_start: 0.8318 (mttp) cc_final: 0.8056 (mmtm) REVERT: H 90 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7219 (mtp85) REVERT: H 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8056 (mmtm) REVERT: H 158 MET cc_start: 0.8919 (mtp) cc_final: 0.8653 (mtp) REVERT: I 90 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7220 (mtp85) REVERT: I 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8057 (mmtm) REVERT: I 158 MET cc_start: 0.8921 (mtp) cc_final: 0.8653 (mtp) REVERT: J 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7225 (mtp85) REVERT: J 157 LYS cc_start: 0.8317 (mttp) cc_final: 0.8054 (mmtm) REVERT: J 158 MET cc_start: 0.8918 (mtp) cc_final: 0.8650 (mtp) REVERT: K 90 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7217 (mtp85) REVERT: K 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8058 (mmtm) REVERT: K 158 MET cc_start: 0.8921 (mtp) cc_final: 0.8653 (mtp) REVERT: L 90 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7214 (mtp85) REVERT: L 157 LYS cc_start: 0.8317 (mttp) cc_final: 0.8050 (mmtm) REVERT: M 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7221 (mtp85) REVERT: M 157 LYS cc_start: 0.8321 (mttp) cc_final: 0.8058 (mmtm) REVERT: M 158 MET cc_start: 0.8920 (mtp) cc_final: 0.8654 (mtp) REVERT: N 90 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7219 (mtp85) REVERT: N 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8058 (mmtm) REVERT: O 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7222 (mtp85) REVERT: O 157 LYS cc_start: 0.8318 (mttp) cc_final: 0.8056 (mmtm) REVERT: O 158 MET cc_start: 0.8919 (mtp) cc_final: 0.8653 (mtp) REVERT: P 90 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7219 (mtp85) REVERT: P 157 LYS cc_start: 0.8317 (mttp) cc_final: 0.8056 (mmtm) REVERT: Q 90 ARG cc_start: 0.7472 (mtt180) cc_final: 0.7213 (mtp85) REVERT: Q 157 LYS cc_start: 0.8315 (mttp) cc_final: 0.8050 (mmtm) REVERT: Q 158 MET cc_start: 0.8919 (mtp) cc_final: 0.8652 (mtp) REVERT: R 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7226 (mtp85) REVERT: R 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8056 (mmtm) REVERT: S 90 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7220 (mtp85) REVERT: S 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8056 (mmtm) REVERT: S 158 MET cc_start: 0.8919 (mtp) cc_final: 0.8653 (mtp) REVERT: T 90 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7222 (mtp85) REVERT: T 157 LYS cc_start: 0.8318 (mttp) cc_final: 0.8055 (mmtm) REVERT: U 90 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7219 (mtp85) REVERT: U 157 LYS cc_start: 0.8320 (mttp) cc_final: 0.8060 (mmtm) REVERT: U 158 MET cc_start: 0.8920 (mtp) cc_final: 0.8656 (mtp) REVERT: V 90 ARG cc_start: 0.7477 (mtt180) cc_final: 0.7215 (mtp85) REVERT: V 157 LYS cc_start: 0.8318 (mttp) cc_final: 0.8056 (mmtm) REVERT: V 158 MET cc_start: 0.8919 (mtp) cc_final: 0.8651 (mtp) REVERT: W 90 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7219 (mtp85) REVERT: W 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8058 (mmtm) REVERT: X 90 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7223 (mtp85) REVERT: X 157 LYS cc_start: 0.8316 (mttp) cc_final: 0.8057 (mmtm) REVERT: X 158 MET cc_start: 0.8920 (mtp) cc_final: 0.8653 (mtp) outliers start: 48 outliers final: 24 residues processed: 912 average time/residue: 1.2189 time to fit residues: 1256.5740 Evaluate side-chains 899 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 875 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 213 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 220 optimal weight: 0.6980 chunk 236 optimal weight: 4.9990 chunk 276 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.177013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.164670 restraints weight = 12682.706| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 0.27 r_work: 0.3712 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 0.90 restraints_weight: 0.2500 r_work: 0.3271 rms_B_bonded: 2.50 restraints_weight: 0.1250 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34920 Z= 0.185 Angle : 0.624 5.384 46992 Z= 0.337 Chirality : 0.038 0.127 4896 Planarity : 0.004 0.024 6192 Dihedral : 4.535 22.907 4560 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.22 % Allowed : 5.33 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.48 (0.13), residues: 4128 helix: 3.51 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.85 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG S 156 TYR 0.016 0.002 TYR Q 137 PHE 0.019 0.003 PHE R 41 TRP 0.012 0.003 TRP O 93 HIS 0.006 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00384 (34920) covalent geometry : angle 0.62355 (46992) hydrogen bonds : bond 0.05546 ( 2640) hydrogen bonds : angle 3.83983 ( 7920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 864 time to evaluate : 1.243 Fit side-chains REVERT: A 90 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7207 (mtp85) REVERT: A 157 LYS cc_start: 0.8368 (mttp) cc_final: 0.8097 (mmtm) REVERT: A 158 MET cc_start: 0.8934 (mtp) cc_final: 0.8628 (mtp) REVERT: B 90 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7206 (mtp85) REVERT: C 90 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7209 (mtp85) REVERT: D 90 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7209 (mtp85) REVERT: D 158 MET cc_start: 0.8918 (mtp) cc_final: 0.8630 (mtp) REVERT: E 90 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7207 (mtp85) REVERT: E 157 LYS cc_start: 0.8366 (mttp) cc_final: 0.8098 (mmtm) REVERT: E 158 MET cc_start: 0.8934 (mtp) cc_final: 0.8635 (mtp) REVERT: F 90 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7207 (mtp85) REVERT: F 158 MET cc_start: 0.8934 (mtp) cc_final: 0.8627 (mtp) REVERT: G 90 ARG cc_start: 0.7472 (mtt180) cc_final: 0.7205 (mtp85) REVERT: H 90 ARG cc_start: 0.7477 (mtt180) cc_final: 0.7211 (mtp85) REVERT: H 158 MET cc_start: 0.8918 (mtp) cc_final: 0.8627 (mtp) REVERT: I 90 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7214 (mtp85) REVERT: I 158 MET cc_start: 0.8921 (mtp) cc_final: 0.8633 (mtp) REVERT: J 90 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7212 (mtp85) REVERT: J 158 MET cc_start: 0.8918 (mtp) cc_final: 0.8626 (mtp) REVERT: K 90 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7211 (mtp85) REVERT: K 158 MET cc_start: 0.8920 (mtp) cc_final: 0.8632 (mtp) REVERT: L 90 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7206 (mtp85) REVERT: M 90 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7213 (mtp85) REVERT: M 158 MET cc_start: 0.8922 (mtp) cc_final: 0.8631 (mtp) REVERT: N 90 ARG cc_start: 0.7471 (mtt180) cc_final: 0.7207 (mtp85) REVERT: O 90 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7212 (mtp85) REVERT: O 158 MET cc_start: 0.8919 (mtp) cc_final: 0.8626 (mtp) REVERT: P 90 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7212 (mtp85) REVERT: Q 90 ARG cc_start: 0.7472 (mtt180) cc_final: 0.7208 (mtp85) REVERT: Q 158 MET cc_start: 0.8917 (mtp) cc_final: 0.8626 (mtp) REVERT: R 90 ARG cc_start: 0.7476 (mtt180) cc_final: 0.7214 (mtp85) REVERT: S 90 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7210 (mtp85) REVERT: S 158 MET cc_start: 0.8920 (mtp) cc_final: 0.8630 (mtp) REVERT: T 90 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7207 (mtp85) REVERT: U 90 ARG cc_start: 0.7471 (mtt180) cc_final: 0.7208 (mtp85) REVERT: U 158 MET cc_start: 0.8919 (mtp) cc_final: 0.8630 (mtp) REVERT: V 90 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7210 (mtp85) REVERT: V 158 MET cc_start: 0.8918 (mtp) cc_final: 0.8626 (mtp) REVERT: W 90 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7207 (mtp85) REVERT: X 90 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7209 (mtp85) REVERT: X 158 MET cc_start: 0.8919 (mtp) cc_final: 0.8631 (mtp) outliers start: 45 outliers final: 24 residues processed: 888 average time/residue: 1.2202 time to fit residues: 1223.3032 Evaluate side-chains 888 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 864 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 337 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 276 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 369 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.176072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.163632 restraints weight = 12739.784| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 0.27 r_work: 0.3700 rms_B_bonded: 0.49 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 0.90 restraints_weight: 0.2500 r_work: 0.3258 rms_B_bonded: 2.51 restraints_weight: 0.1250 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 34920 Z= 0.219 Angle : 0.668 5.725 46992 Z= 0.365 Chirality : 0.039 0.150 4896 Planarity : 0.004 0.031 6192 Dihedral : 4.571 22.402 4560 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.97 % Allowed : 6.49 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.28 (0.13), residues: 4128 helix: 3.36 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.77 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 156 TYR 0.016 0.003 TYR H 137 PHE 0.020 0.003 PHE V 41 TRP 0.014 0.004 TRP V 93 HIS 0.007 0.002 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00457 (34920) covalent geometry : angle 0.66801 (46992) hydrogen bonds : bond 0.05814 ( 2640) hydrogen bonds : angle 3.93475 ( 7920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 878 time to evaluate : 1.610 Fit side-chains REVERT: D 158 MET cc_start: 0.8942 (mtp) cc_final: 0.8682 (mtp) REVERT: H 158 MET cc_start: 0.8942 (mtp) cc_final: 0.8677 (mtp) REVERT: I 158 MET cc_start: 0.8940 (mtp) cc_final: 0.8680 (mtp) REVERT: J 158 MET cc_start: 0.8942 (mtp) cc_final: 0.8678 (mtp) REVERT: K 158 MET cc_start: 0.8945 (mtp) cc_final: 0.8682 (mtp) REVERT: M 158 MET cc_start: 0.8944 (mtp) cc_final: 0.8683 (mtp) REVERT: Q 158 MET cc_start: 0.8941 (mtp) cc_final: 0.8680 (mtp) REVERT: S 158 MET cc_start: 0.8943 (mtp) cc_final: 0.8678 (mtp) REVERT: U 158 MET cc_start: 0.8941 (mtp) cc_final: 0.8678 (mtp) REVERT: V 158 MET cc_start: 0.8944 (mtp) cc_final: 0.8689 (mtp) REVERT: X 158 MET cc_start: 0.8945 (mtp) cc_final: 0.8682 (mtp) outliers start: 36 outliers final: 24 residues processed: 902 average time/residue: 1.2296 time to fit residues: 1251.9630 Evaluate side-chains 885 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 861 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 13 optimal weight: 9.9990 chunk 295 optimal weight: 5.9990 chunk 238 optimal weight: 20.0000 chunk 279 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 302 optimal weight: 1.9990 chunk 299 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 190 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.178141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.165904 restraints weight = 12761.048| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 0.27 r_work: 0.3726 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 0.90 restraints_weight: 0.2500 r_work: 0.3288 rms_B_bonded: 2.51 restraints_weight: 0.1250 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34920 Z= 0.155 Angle : 0.576 5.599 46992 Z= 0.312 Chirality : 0.037 0.119 4896 Planarity : 0.004 0.022 6192 Dihedral : 4.488 23.103 4560 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.65 % Allowed : 6.82 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.53 (0.13), residues: 4128 helix: 3.54 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.85 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 90 TYR 0.014 0.002 TYR V 136 PHE 0.017 0.003 PHE A 41 TRP 0.014 0.003 TRP I 93 HIS 0.005 0.001 HIS I 128 Details of bonding type rmsd covalent geometry : bond 0.00320 (34920) covalent geometry : angle 0.57634 (46992) hydrogen bonds : bond 0.05183 ( 2640) hydrogen bonds : angle 3.75306 ( 7920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 870 time to evaluate : 1.781 Fit side-chains REVERT: A 157 LYS cc_start: 0.8327 (mttp) cc_final: 0.8063 (mmtm) REVERT: B 157 LYS cc_start: 0.8270 (mttp) cc_final: 0.8028 (mmtm) REVERT: C 157 LYS cc_start: 0.8276 (mttp) cc_final: 0.8034 (mmtm) REVERT: D 157 LYS cc_start: 0.8315 (mttp) cc_final: 0.8052 (mmtm) REVERT: D 158 MET cc_start: 0.8876 (mtp) cc_final: 0.8559 (mtp) REVERT: E 157 LYS cc_start: 0.8328 (mttp) cc_final: 0.8064 (mmtm) REVERT: F 157 LYS cc_start: 0.8327 (mttp) cc_final: 0.8065 (mmtm) REVERT: G 157 LYS cc_start: 0.8270 (mttp) cc_final: 0.8030 (mmtm) REVERT: H 157 LYS cc_start: 0.8324 (mttp) cc_final: 0.8059 (mmtm) REVERT: H 158 MET cc_start: 0.8876 (mtp) cc_final: 0.8553 (mtp) REVERT: H 165 MET cc_start: 0.8311 (tpp) cc_final: 0.8084 (tpp) REVERT: I 157 LYS cc_start: 0.8324 (mttp) cc_final: 0.8055 (mmtm) REVERT: I 158 MET cc_start: 0.8875 (mtp) cc_final: 0.8560 (mtp) REVERT: J 157 LYS cc_start: 0.8322 (mttp) cc_final: 0.8056 (mmtm) REVERT: J 158 MET cc_start: 0.8874 (mtp) cc_final: 0.8554 (mtp) REVERT: K 157 LYS cc_start: 0.8311 (mttp) cc_final: 0.8049 (mmtm) REVERT: K 158 MET cc_start: 0.8877 (mtp) cc_final: 0.8553 (mtp) REVERT: K 165 MET cc_start: 0.8314 (tpp) cc_final: 0.8088 (tpp) REVERT: L 157 LYS cc_start: 0.8273 (mttp) cc_final: 0.8029 (mmtm) REVERT: M 157 LYS cc_start: 0.8326 (mttp) cc_final: 0.8057 (mmtm) REVERT: M 158 MET cc_start: 0.8874 (mtp) cc_final: 0.8559 (mtp) REVERT: N 157 LYS cc_start: 0.8274 (mttp) cc_final: 0.8034 (mmtm) REVERT: N 165 MET cc_start: 0.8324 (tpp) cc_final: 0.8103 (tpp) REVERT: O 157 LYS cc_start: 0.8328 (mttp) cc_final: 0.8067 (mmtm) REVERT: O 165 MET cc_start: 0.8337 (tpp) cc_final: 0.8113 (tpp) REVERT: P 157 LYS cc_start: 0.8274 (mttp) cc_final: 0.8033 (mmtm) REVERT: Q 157 LYS cc_start: 0.8314 (mttp) cc_final: 0.8046 (mmtm) REVERT: Q 158 MET cc_start: 0.8875 (mtp) cc_final: 0.8560 (mtp) REVERT: R 157 LYS cc_start: 0.8278 (mttp) cc_final: 0.8035 (mmtm) REVERT: S 157 LYS cc_start: 0.8323 (mttp) cc_final: 0.8056 (mmtm) REVERT: S 158 MET cc_start: 0.8879 (mtp) cc_final: 0.8554 (mtp) REVERT: S 165 MET cc_start: 0.8320 (tpp) cc_final: 0.8094 (tpp) REVERT: T 157 LYS cc_start: 0.8275 (mttp) cc_final: 0.8031 (mmtm) REVERT: U 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8052 (mmtm) REVERT: U 158 MET cc_start: 0.8876 (mtp) cc_final: 0.8553 (mtp) REVERT: U 165 MET cc_start: 0.8318 (tpp) cc_final: 0.8093 (tpp) REVERT: V 158 MET cc_start: 0.8875 (mtp) cc_final: 0.8572 (mtp) REVERT: W 157 LYS cc_start: 0.8272 (mttp) cc_final: 0.8031 (mmtm) REVERT: W 165 MET cc_start: 0.8323 (tpp) cc_final: 0.8100 (tpp) REVERT: X 157 LYS cc_start: 0.8319 (mttp) cc_final: 0.8054 (mmtm) REVERT: X 158 MET cc_start: 0.8874 (mtp) cc_final: 0.8553 (mtp) REVERT: X 165 MET cc_start: 0.8322 (tpp) cc_final: 0.8095 (tpp) outliers start: 24 outliers final: 24 residues processed: 894 average time/residue: 1.1720 time to fit residues: 1186.5280 Evaluate side-chains 894 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 870 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 238 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 303 optimal weight: 0.7980 chunk 365 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.176204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.163941 restraints weight = 12743.562| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 0.27 r_work: 0.3706 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.3264 rms_B_bonded: 2.49 restraints_weight: 0.1250 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 34920 Z= 0.216 Angle : 0.666 6.179 46992 Z= 0.363 Chirality : 0.039 0.143 4896 Planarity : 0.004 0.023 6192 Dihedral : 4.567 22.546 4560 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 6.25 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.29 (0.13), residues: 4128 helix: 3.42 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.67 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG V 156 TYR 0.016 0.002 TYR F 137 PHE 0.020 0.003 PHE M 41 TRP 0.012 0.004 TRP W 93 HIS 0.007 0.002 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00456 (34920) covalent geometry : angle 0.66646 (46992) hydrogen bonds : bond 0.05791 ( 2640) hydrogen bonds : angle 3.93442 ( 7920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 877 time to evaluate : 1.649 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 901 average time/residue: 1.2626 time to fit residues: 1284.4287 Evaluate side-chains 884 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 860 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 315 optimal weight: 5.9990 chunk 323 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 225 optimal weight: 0.6980 chunk 368 optimal weight: 4.9990 chunk 390 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 chunk 362 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.177003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.164799 restraints weight = 12807.611| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 0.27 r_work: 0.3717 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.3276 rms_B_bonded: 2.49 restraints_weight: 0.1250 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34920 Z= 0.187 Angle : 0.626 5.683 46992 Z= 0.340 Chirality : 0.038 0.123 4896 Planarity : 0.004 0.020 6192 Dihedral : 4.543 22.994 4560 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.65 % Allowed : 5.79 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.33 (0.13), residues: 4128 helix: 3.44 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.69 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 156 TYR 0.015 0.002 TYR V 137 PHE 0.018 0.003 PHE V 41 TRP 0.013 0.004 TRP N 93 HIS 0.006 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00391 (34920) covalent geometry : angle 0.62572 (46992) hydrogen bonds : bond 0.05524 ( 2640) hydrogen bonds : angle 3.86545 ( 7920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 856 time to evaluate : 1.609 Fit side-chains REVERT: A 165 MET cc_start: 0.8330 (tpp) cc_final: 0.8101 (tpp) REVERT: B 165 MET cc_start: 0.8333 (tpp) cc_final: 0.8106 (tpp) REVERT: C 165 MET cc_start: 0.8334 (tpp) cc_final: 0.8105 (tpp) REVERT: D 165 MET cc_start: 0.8332 (tpp) cc_final: 0.8102 (tpp) REVERT: E 165 MET cc_start: 0.8332 (tpp) cc_final: 0.8103 (tpp) REVERT: F 165 MET cc_start: 0.8328 (tpp) cc_final: 0.8097 (tpp) REVERT: G 165 MET cc_start: 0.8343 (tpp) cc_final: 0.8114 (tpp) REVERT: I 165 MET cc_start: 0.8335 (tpp) cc_final: 0.8103 (tpp) REVERT: J 165 MET cc_start: 0.8334 (tpp) cc_final: 0.8105 (tpp) REVERT: K 165 MET cc_start: 0.8355 (tpp) cc_final: 0.8147 (tpp) REVERT: L 165 MET cc_start: 0.8334 (tpp) cc_final: 0.8105 (tpp) REVERT: N 165 MET cc_start: 0.8363 (tpp) cc_final: 0.8130 (tpp) REVERT: P 165 MET cc_start: 0.8335 (tpp) cc_final: 0.8108 (tpp) REVERT: Q 165 MET cc_start: 0.8335 (tpp) cc_final: 0.8104 (tpp) REVERT: R 165 MET cc_start: 0.8357 (tpp) cc_final: 0.8124 (tpp) REVERT: T 165 MET cc_start: 0.8340 (tpp) cc_final: 0.8113 (tpp) REVERT: V 165 MET cc_start: 0.8343 (tpp) cc_final: 0.8112 (tpp) REVERT: W 165 MET cc_start: 0.8354 (tpp) cc_final: 0.8118 (tpp) outliers start: 24 outliers final: 24 residues processed: 880 average time/residue: 1.2583 time to fit residues: 1250.1661 Evaluate side-chains 880 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 856 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 106 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 379 optimal weight: 5.9990 chunk 359 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 405 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 340 optimal weight: 0.5980 chunk 377 optimal weight: 0.7980 chunk 85 optimal weight: 20.0000 chunk 398 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.177276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.165130 restraints weight = 12748.738| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 0.27 r_work: 0.3721 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.3280 rms_B_bonded: 2.49 restraints_weight: 0.1250 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34920 Z= 0.180 Angle : 0.618 5.603 46992 Z= 0.336 Chirality : 0.038 0.122 4896 Planarity : 0.004 0.021 6192 Dihedral : 4.534 22.948 4560 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 5.25 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.37 (0.13), residues: 4128 helix: 3.48 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.68 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 156 TYR 0.014 0.002 TYR D 137 PHE 0.017 0.003 PHE P 41 TRP 0.013 0.004 TRP T 93 HIS 0.005 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00376 (34920) covalent geometry : angle 0.61816 (46992) hydrogen bonds : bond 0.05466 ( 2640) hydrogen bonds : angle 3.84901 ( 7920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 876 time to evaluate : 1.577 Fit side-chains REVERT: A 165 MET cc_start: 0.8345 (tpp) cc_final: 0.8120 (tpp) REVERT: B 165 MET cc_start: 0.8348 (tpp) cc_final: 0.8126 (tpp) REVERT: C 165 MET cc_start: 0.8345 (tpp) cc_final: 0.8121 (tpp) REVERT: D 165 MET cc_start: 0.8349 (tpp) cc_final: 0.8123 (tpp) REVERT: E 165 MET cc_start: 0.8345 (tpp) cc_final: 0.8120 (tpp) REVERT: F 165 MET cc_start: 0.8341 (tpp) cc_final: 0.8116 (tpp) REVERT: G 165 MET cc_start: 0.8293 (tpp) cc_final: 0.8065 (tpp) REVERT: H 165 MET cc_start: 0.8350 (tpp) cc_final: 0.8112 (tpp) REVERT: I 165 MET cc_start: 0.8350 (tpp) cc_final: 0.8124 (tpp) REVERT: J 165 MET cc_start: 0.8350 (tpp) cc_final: 0.8127 (tpp) REVERT: K 165 MET cc_start: 0.8358 (tpp) cc_final: 0.8122 (tpp) REVERT: L 165 MET cc_start: 0.8322 (tpp) cc_final: 0.8095 (tpp) REVERT: N 165 MET cc_start: 0.8359 (tpp) cc_final: 0.8126 (tpp) REVERT: O 165 MET cc_start: 0.8366 (tpp) cc_final: 0.8132 (tpp) REVERT: P 165 MET cc_start: 0.8349 (tpp) cc_final: 0.8127 (tpp) REVERT: Q 165 MET cc_start: 0.8346 (tpp) cc_final: 0.8121 (tpp) REVERT: R 165 MET cc_start: 0.8357 (tpp) cc_final: 0.8124 (tpp) REVERT: S 165 MET cc_start: 0.8359 (tpp) cc_final: 0.8122 (tpp) REVERT: T 165 MET cc_start: 0.8291 (tpp) cc_final: 0.8063 (tpp) REVERT: U 165 MET cc_start: 0.8358 (tpp) cc_final: 0.8121 (tpp) REVERT: V 165 MET cc_start: 0.8293 (tpp) cc_final: 0.8061 (tpp) REVERT: W 165 MET cc_start: 0.8352 (tpp) cc_final: 0.8117 (tpp) REVERT: X 165 MET cc_start: 0.8351 (tpp) cc_final: 0.8113 (tpp) outliers start: 24 outliers final: 24 residues processed: 900 average time/residue: 1.0781 time to fit residues: 1100.4128 Evaluate side-chains 900 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 876 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain U residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 137 optimal weight: 9.9990 chunk 301 optimal weight: 4.9990 chunk 315 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 382 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 369 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 337 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN H 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.176858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.164630 restraints weight = 12775.202| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 0.27 r_work: 0.3715 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.3272 rms_B_bonded: 2.49 restraints_weight: 0.1250 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34920 Z= 0.201 Angle : 0.655 6.004 46992 Z= 0.357 Chirality : 0.039 0.135 4896 Planarity : 0.004 0.020 6192 Dihedral : 4.553 22.676 4560 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 5.33 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.23 (0.13), residues: 4128 helix: 3.37 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.64 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 156 TYR 0.016 0.002 TYR I 137 PHE 0.019 0.003 PHE W 41 TRP 0.013 0.004 TRP S 93 HIS 0.006 0.002 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00423 (34920) covalent geometry : angle 0.65467 (46992) hydrogen bonds : bond 0.05672 ( 2640) hydrogen bonds : angle 3.92072 ( 7920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33211.14 seconds wall clock time: 562 minutes 8.02 seconds (33728.02 seconds total)