Starting phenix.real_space_refine on Mon Dec 30 22:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f54_28860/12_2024/8f54_28860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f54_28860/12_2024/8f54_28860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f54_28860/12_2024/8f54_28860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f54_28860/12_2024/8f54_28860.map" model { file = "/net/cci-nas-00/data/ceres_data/8f54_28860/12_2024/8f54_28860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f54_28860/12_2024/8f54_28860.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.154 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: 5 Type Number sf(0) Gaussians S 120 5.16 5 C 21420 2.51 5 N 5760 2.21 5 O 5820 1.98 5 H 33840 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 66960 Number of models: 1 Model: "" Number of chains: 60 Chain: "L" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "o" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "p" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "A" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "q" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "S" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "r" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "C" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "D" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "T" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "E" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "B" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "s" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "i" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "k" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "U" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "m" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "g" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "t" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "N" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "O" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "V" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "P" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "F" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "Q" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "j" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "l" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "G" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "n" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "h" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "R" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "J" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "M" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "I" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "u" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "v" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "w" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "W" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "x" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "X" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "y" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "Y" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "z" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "Z" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "0" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "a" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "1" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "2" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "c" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "3" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "d" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "4" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "5" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "f" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "7" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "6" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1116 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Time building chain proxies: 25.77, per 1000 atoms: 0.38 Number of scatterers: 66960 At special positions: 0 Unit cell: (157.08, 157.08, 157.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 O 5820 8.00 N 5760 7.00 C 21420 6.00 H 33840 1.00 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: 14.54 Conformation dependent library (CDL) restraints added in 3.8 seconds 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'L' and resid 1 through 20 Processing helix chain 'L' and resid 22 through 37 Processing helix chain 'L' and resid 39 through 51 removed outlier: 3.998A pdb=" N ALA L 43 " --> pdb=" O PRO L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 65 Processing helix chain 'o' and resid 2 through 20 Processing helix chain 'o' and resid 22 through 37 Processing helix chain 'o' and resid 39 through 51 removed outlier: 3.916A pdb=" N ALA o 43 " --> pdb=" O PRO o 39 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 65 Processing helix chain 'p' and resid 2 through 20 Processing helix chain 'p' and resid 22 through 37 Processing helix chain 'p' and resid 39 through 51 removed outlier: 3.974A pdb=" N ALA p 43 " --> pdb=" O PRO p 39 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 65 Processing helix chain 'A' and resid 2 through 20 Processing helix chain 'A' and resid 22 through 37 Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.932A pdb=" N ALA A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'q' and resid 2 through 20 Processing helix chain 'q' and resid 22 through 37 Processing helix chain 'q' and resid 39 through 52 removed outlier: 3.967A pdb=" N ALA q 43 " --> pdb=" O PRO q 39 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY q 52 " --> pdb=" O LEU q 48 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 65 Processing helix chain 'S' and resid 2 through 20 Processing helix chain 'S' and resid 22 through 37 Processing helix chain 'S' and resid 39 through 51 removed outlier: 3.902A pdb=" N ALA S 43 " --> pdb=" O PRO S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 65 Processing helix chain 'r' and resid 2 through 20 Processing helix chain 'r' and resid 22 through 37 Processing helix chain 'r' and resid 39 through 51 removed outlier: 3.930A pdb=" N ALA r 43 " --> pdb=" O PRO r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 65 Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 39 through 51 removed outlier: 3.975A pdb=" N ALA C 43 " --> pdb=" O PRO C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 65 Processing helix chain 'D' and resid 2 through 20 Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 39 through 51 removed outlier: 3.955A pdb=" N ALA D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 65 Processing helix chain 'T' and resid 2 through 20 Processing helix chain 'T' and resid 22 through 37 Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.998A pdb=" N ALA T 43 " --> pdb=" O PRO T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 65 Processing helix chain 'E' and resid 2 through 20 Processing helix chain 'E' and resid 22 through 37 Processing helix chain 'E' and resid 39 through 51 removed outlier: 3.950A pdb=" N ALA E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 65 Processing helix chain 'B' and resid 2 through 20 Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 39 through 52 removed outlier: 3.955A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 's' and resid 2 through 20 Processing helix chain 's' and resid 22 through 37 Processing helix chain 's' and resid 39 through 51 removed outlier: 3.940A pdb=" N ALA s 43 " --> pdb=" O PRO s 39 " (cutoff:3.500A) Processing helix chain 's' and resid 53 through 65 Processing helix chain 'i' and resid 2 through 20 Processing helix chain 'i' and resid 22 through 37 Processing helix chain 'i' and resid 39 through 51 removed outlier: 3.981A pdb=" N ALA i 43 " --> pdb=" O PRO i 39 " (cutoff:3.500A) Processing helix chain 'i' and resid 53 through 65 Processing helix chain 'k' and resid 2 through 20 Processing helix chain 'k' and resid 22 through 37 Processing helix chain 'k' and resid 39 through 51 removed outlier: 3.967A pdb=" N ALA k 43 " --> pdb=" O PRO k 39 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 65 Processing helix chain 'U' and resid 2 through 20 Processing helix chain 'U' and resid 22 through 37 Processing helix chain 'U' and resid 39 through 51 removed outlier: 3.993A pdb=" N ALA U 43 " --> pdb=" O PRO U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 65 Processing helix chain 'm' and resid 2 through 20 Processing helix chain 'm' and resid 22 through 37 Processing helix chain 'm' and resid 39 through 51 removed outlier: 3.970A pdb=" N ALA m 43 " --> pdb=" O PRO m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 53 through 65 Processing helix chain 'g' and resid 2 through 20 Processing helix chain 'g' and resid 22 through 37 Processing helix chain 'g' and resid 39 through 51 removed outlier: 3.973A pdb=" N ALA g 43 " --> pdb=" O PRO g 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 65 Processing helix chain 't' and resid 2 through 20 Processing helix chain 't' and resid 22 through 37 Processing helix chain 't' and resid 39 through 51 removed outlier: 3.980A pdb=" N ALA t 43 " --> pdb=" O PRO t 39 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 65 Processing helix chain 'N' and resid 2 through 20 Processing helix chain 'N' and resid 22 through 37 Processing helix chain 'N' and resid 39 through 51 removed outlier: 3.973A pdb=" N ALA N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 65 Processing helix chain 'O' and resid 2 through 20 Processing helix chain 'O' and resid 22 through 37 Processing helix chain 'O' and resid 39 through 51 removed outlier: 3.978A pdb=" N ALA O 43 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 65 Processing helix chain 'V' and resid 2 through 20 Processing helix chain 'V' and resid 22 through 37 Processing helix chain 'V' and resid 39 through 52 removed outlier: 4.008A pdb=" N ALA V 43 " --> pdb=" O PRO V 39 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 65 Processing helix chain 'P' and resid 2 through 20 Processing helix chain 'P' and resid 22 through 37 Processing helix chain 'P' and resid 39 through 51 removed outlier: 3.952A pdb=" N ALA P 43 " --> pdb=" O PRO P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 65 Processing helix chain 'F' and resid 2 through 20 Processing helix chain 'F' and resid 22 through 37 Processing helix chain 'F' and resid 39 through 51 removed outlier: 3.972A pdb=" N ALA F 43 " --> pdb=" O PRO F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 Processing helix chain 'Q' and resid 2 through 20 Processing helix chain 'Q' and resid 22 through 37 Processing helix chain 'Q' and resid 39 through 51 removed outlier: 3.963A pdb=" N ALA Q 43 " --> pdb=" O PRO Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 65 Processing helix chain 'j' and resid 2 through 20 Processing helix chain 'j' and resid 22 through 37 Processing helix chain 'j' and resid 39 through 51 removed outlier: 3.988A pdb=" N ALA j 43 " --> pdb=" O PRO j 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 53 through 65 Processing helix chain 'l' and resid 2 through 20 Processing helix chain 'l' and resid 22 through 37 Processing helix chain 'l' and resid 39 through 51 removed outlier: 3.964A pdb=" N ALA l 43 " --> pdb=" O PRO l 39 " (cutoff:3.500A) Processing helix chain 'l' and resid 53 through 65 Processing helix chain 'G' and resid 2 through 20 Processing helix chain 'G' and resid 22 through 37 Processing helix chain 'G' and resid 39 through 51 removed outlier: 4.001A pdb=" N ALA G 43 " --> pdb=" O PRO G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 65 Processing helix chain 'n' and resid 2 through 20 Processing helix chain 'n' and resid 22 through 37 Processing helix chain 'n' and resid 39 through 51 removed outlier: 3.939A pdb=" N ALA n 43 " --> pdb=" O PRO n 39 " (cutoff:3.500A) Processing helix chain 'n' and resid 53 through 65 Processing helix chain 'h' and resid 2 through 20 Processing helix chain 'h' and resid 22 through 37 Processing helix chain 'h' and resid 39 through 51 removed outlier: 3.959A pdb=" N ALA h 43 " --> pdb=" O PRO h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 53 through 65 Processing helix chain 'R' and resid 2 through 20 Processing helix chain 'R' and resid 22 through 37 Processing helix chain 'R' and resid 39 through 52 removed outlier: 4.008A pdb=" N ALA R 43 " --> pdb=" O PRO R 39 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 65 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 22 through 37 Processing helix chain 'J' and resid 39 through 51 removed outlier: 3.940A pdb=" N ALA J 43 " --> pdb=" O PRO J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 65 Processing helix chain 'K' and resid 2 through 20 Processing helix chain 'K' and resid 22 through 37 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.963A pdb=" N ALA K 43 " --> pdb=" O PRO K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 65 Processing helix chain 'H' and resid 2 through 20 Processing helix chain 'H' and resid 22 through 37 Processing helix chain 'H' and resid 39 through 51 removed outlier: 3.939A pdb=" N ALA H 43 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'M' and resid 2 through 20 Processing helix chain 'M' and resid 22 through 37 Processing helix chain 'M' and resid 39 through 51 removed outlier: 4.003A pdb=" N ALA M 43 " --> pdb=" O PRO M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 65 Processing helix chain 'I' and resid 2 through 20 Processing helix chain 'I' and resid 22 through 37 Processing helix chain 'I' and resid 39 through 51 removed outlier: 3.942A pdb=" N ALA I 43 " --> pdb=" O PRO I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 65 Processing helix chain 'u' and resid 2 through 20 Processing helix chain 'u' and resid 22 through 37 Processing helix chain 'u' and resid 39 through 51 removed outlier: 3.989A pdb=" N ALA u 43 " --> pdb=" O PRO u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 65 Processing helix chain 'v' and resid 2 through 20 Processing helix chain 'v' and resid 22 through 37 Processing helix chain 'v' and resid 39 through 51 removed outlier: 3.960A pdb=" N ALA v 43 " --> pdb=" O PRO v 39 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 65 Processing helix chain 'w' and resid 2 through 20 Processing helix chain 'w' and resid 22 through 37 Processing helix chain 'w' and resid 39 through 51 removed outlier: 3.978A pdb=" N ALA w 43 " --> pdb=" O PRO w 39 " (cutoff:3.500A) Processing helix chain 'w' and resid 53 through 65 Processing helix chain 'W' and resid 2 through 20 Processing helix chain 'W' and resid 22 through 37 Processing helix chain 'W' and resid 39 through 51 removed outlier: 3.959A pdb=" N ALA W 43 " --> pdb=" O PRO W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 65 Processing helix chain 'x' and resid 2 through 20 Processing helix chain 'x' and resid 22 through 37 Processing helix chain 'x' and resid 39 through 51 removed outlier: 4.015A pdb=" N ALA x 43 " --> pdb=" O PRO x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 53 through 65 Processing helix chain 'X' and resid 2 through 20 Processing helix chain 'X' and resid 22 through 37 Processing helix chain 'X' and resid 39 through 51 removed outlier: 3.960A pdb=" N ALA X 43 " --> pdb=" O PRO X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 65 Processing helix chain 'y' and resid 2 through 20 Processing helix chain 'y' and resid 22 through 37 Processing helix chain 'y' and resid 39 through 51 removed outlier: 3.988A pdb=" N ALA y 43 " --> pdb=" O PRO y 39 " (cutoff:3.500A) Processing helix chain 'y' and resid 53 through 65 Processing helix chain 'Y' and resid 2 through 20 Processing helix chain 'Y' and resid 22 through 37 Processing helix chain 'Y' and resid 39 through 51 removed outlier: 3.992A pdb=" N ALA Y 43 " --> pdb=" O PRO Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 65 Processing helix chain 'z' and resid 2 through 20 Processing helix chain 'z' and resid 22 through 37 Processing helix chain 'z' and resid 39 through 51 removed outlier: 3.990A pdb=" N ALA z 43 " --> pdb=" O PRO z 39 " (cutoff:3.500A) Processing helix chain 'z' and resid 53 through 65 Processing helix chain 'Z' and resid 2 through 20 Processing helix chain 'Z' and resid 22 through 37 Processing helix chain 'Z' and resid 39 through 51 removed outlier: 3.960A pdb=" N ALA Z 43 " --> pdb=" O PRO Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 65 Processing helix chain '0' and resid 2 through 20 Processing helix chain '0' and resid 22 through 37 Processing helix chain '0' and resid 39 through 51 removed outlier: 3.949A pdb=" N ALA 0 43 " --> pdb=" O PRO 0 39 " (cutoff:3.500A) Processing helix chain '0' and resid 53 through 65 Processing helix chain 'a' and resid 2 through 20 Processing helix chain 'a' and resid 22 through 37 Processing helix chain 'a' and resid 39 through 51 removed outlier: 4.039A pdb=" N ALA a 43 " --> pdb=" O PRO a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 65 Processing helix chain '1' and resid 2 through 20 Processing helix chain '1' and resid 22 through 37 Processing helix chain '1' and resid 39 through 51 removed outlier: 3.927A pdb=" N ALA 1 43 " --> pdb=" O PRO 1 39 " (cutoff:3.500A) Processing helix chain '1' and resid 53 through 65 Processing helix chain 'b' and resid 2 through 20 Processing helix chain 'b' and resid 22 through 37 Processing helix chain 'b' and resid 39 through 51 removed outlier: 4.012A pdb=" N ALA b 43 " --> pdb=" O PRO b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 65 Processing helix chain '2' and resid 2 through 20 Processing helix chain '2' and resid 22 through 37 Processing helix chain '2' and resid 39 through 52 removed outlier: 3.987A pdb=" N ALA 2 43 " --> pdb=" O PRO 2 39 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY 2 52 " --> pdb=" O LEU 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 53 through 65 Processing helix chain 'c' and resid 2 through 20 Processing helix chain 'c' and resid 22 through 37 Processing helix chain 'c' and resid 39 through 51 removed outlier: 3.998A pdb=" N ALA c 43 " --> pdb=" O PRO c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 65 Processing helix chain '3' and resid 2 through 20 Processing helix chain '3' and resid 22 through 37 Processing helix chain '3' and resid 39 through 51 removed outlier: 3.911A pdb=" N ALA 3 43 " --> pdb=" O PRO 3 39 " (cutoff:3.500A) Processing helix chain '3' and resid 53 through 65 Processing helix chain 'd' and resid 2 through 20 Processing helix chain 'd' and resid 22 through 37 Processing helix chain 'd' and resid 39 through 51 removed outlier: 3.976A pdb=" N ALA d 43 " --> pdb=" O PRO d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 65 Processing helix chain '4' and resid 2 through 20 Processing helix chain '4' and resid 22 through 37 Processing helix chain '4' and resid 39 through 51 removed outlier: 3.979A pdb=" N ALA 4 43 " --> pdb=" O PRO 4 39 " (cutoff:3.500A) Processing helix chain '4' and resid 53 through 65 Processing helix chain 'e' and resid 2 through 20 Processing helix chain 'e' and resid 22 through 37 Processing helix chain 'e' and resid 39 through 51 removed outlier: 3.956A pdb=" N ALA e 43 " --> pdb=" O PRO e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 53 through 65 Processing helix chain '5' and resid 2 through 20 Processing helix chain '5' and resid 22 through 36 Processing helix chain '5' and resid 39 through 51 removed outlier: 4.018A pdb=" N ALA 5 43 " --> pdb=" O PRO 5 39 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 65 Processing helix chain 'f' and resid 2 through 20 Processing helix chain 'f' and resid 22 through 37 Processing helix chain 'f' and resid 39 through 51 removed outlier: 3.987A pdb=" N ALA f 43 " --> pdb=" O PRO f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 53 through 65 Processing helix chain '7' and resid 2 through 20 Processing helix chain '7' and resid 22 through 37 Processing helix chain '7' and resid 39 through 51 removed outlier: 3.963A pdb=" N ALA 7 43 " --> pdb=" O PRO 7 39 " (cutoff:3.500A) Processing helix chain '7' and resid 53 through 65 Processing helix chain '6' and resid 2 through 20 Processing helix chain '6' and resid 22 through 37 Processing helix chain '6' and resid 39 through 51 removed outlier: 3.983A pdb=" N ALA 6 43 " --> pdb=" O PRO 6 39 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 65 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: 23.70 Time building geometry restraints manager: 17.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 33840 1.03 - 1.23: 0 1.23 - 1.42: 13920 1.42 - 1.61: 19680 1.61 - 1.80: 240 Bond restraints: 67680 Sorted by residual: bond pdb=" CB PRO m 1 " pdb=" CG PRO m 1 " ideal model delta sigma weight residual 1.492 1.521 -0.029 5.00e-02 4.00e+02 3.37e-01 bond pdb=" CB PRO S 1 " pdb=" CG PRO S 1 " ideal model delta sigma weight residual 1.492 1.520 -0.028 5.00e-02 4.00e+02 3.22e-01 bond pdb=" CB PRO i 1 " pdb=" CG PRO i 1 " ideal model delta sigma weight residual 1.492 1.520 -0.028 5.00e-02 4.00e+02 3.18e-01 bond pdb=" CB PRO s 1 " pdb=" CG PRO s 1 " ideal model delta sigma weight residual 1.492 1.520 -0.028 5.00e-02 4.00e+02 3.10e-01 bond pdb=" CB PRO e 1 " pdb=" CG PRO e 1 " ideal model delta sigma weight residual 1.492 1.519 -0.027 5.00e-02 4.00e+02 3.01e-01 ... (remaining 67675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.73: 104388 0.73 - 1.45: 16808 1.45 - 2.18: 1540 2.18 - 2.91: 231 2.91 - 3.63: 93 Bond angle restraints: 123060 Sorted by residual: angle pdb=" CA ARG B 50 " pdb=" CB ARG B 50 " pdb=" CG ARG B 50 " ideal model delta sigma weight residual 114.10 111.40 2.70 2.00e+00 2.50e-01 1.82e+00 angle pdb=" CA ARG Y 50 " pdb=" CB ARG Y 50 " pdb=" CG ARG Y 50 " ideal model delta sigma weight residual 114.10 111.44 2.66 2.00e+00 2.50e-01 1.77e+00 angle pdb=" CA ARG c 50 " pdb=" CB ARG c 50 " pdb=" CG ARG c 50 " ideal model delta sigma weight residual 114.10 111.44 2.66 2.00e+00 2.50e-01 1.76e+00 angle pdb=" CA ARG h 50 " pdb=" CB ARG h 50 " pdb=" CG ARG h 50 " ideal model delta sigma weight residual 114.10 111.44 2.66 2.00e+00 2.50e-01 1.76e+00 angle pdb=" CA ARG K 50 " pdb=" CB ARG K 50 " pdb=" CG ARG K 50 " ideal model delta sigma weight residual 114.10 111.45 2.65 2.00e+00 2.50e-01 1.75e+00 ... (remaining 123055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 28919 17.62 - 35.25: 1268 35.25 - 52.87: 513 52.87 - 70.50: 105 70.50 - 88.12: 35 Dihedral angle restraints: 30840 sinusoidal: 17160 harmonic: 13680 Sorted by residual: dihedral pdb=" CB GLU a 8 " pdb=" CG GLU a 8 " pdb=" CD GLU a 8 " pdb=" OE1 GLU a 8 " ideal model delta sinusoidal sigma weight residual 0.00 67.15 -67.15 1 3.00e+01 1.11e-03 6.52e+00 dihedral pdb=" CB GLU O 8 " pdb=" CG GLU O 8 " pdb=" CD GLU O 8 " pdb=" OE1 GLU O 8 " ideal model delta sinusoidal sigma weight residual 0.00 64.75 -64.75 1 3.00e+01 1.11e-03 6.12e+00 dihedral pdb=" CB GLU p 8 " pdb=" CG GLU p 8 " pdb=" CD GLU p 8 " pdb=" OE1 GLU p 8 " ideal model delta sinusoidal sigma weight residual 0.00 64.57 -64.57 1 3.00e+01 1.11e-03 6.09e+00 ... (remaining 30837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 3058 0.022 - 0.043: 1063 0.043 - 0.065: 270 0.065 - 0.086: 460 0.086 - 0.108: 129 Chirality restraints: 4980 Sorted by residual: chirality pdb=" CA PRO 7 39 " pdb=" N PRO 7 39 " pdb=" C PRO 7 39 " pdb=" CB PRO 7 39 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.90e-01 chirality pdb=" CA PRO d 39 " pdb=" N PRO d 39 " pdb=" C PRO d 39 " pdb=" CB PRO d 39 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.89e-01 chirality pdb=" CA PRO 4 39 " pdb=" N PRO 4 39 " pdb=" C PRO 4 39 " pdb=" CB PRO 4 39 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.86e-01 ... (remaining 4977 not shown) Planarity restraints: 9600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 22 " -0.013 5.00e-02 4.00e+02 2.03e-02 6.62e-01 pdb=" N PRO L 23 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO L 23 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO L 23 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP V 38 " 0.013 5.00e-02 4.00e+02 2.03e-02 6.59e-01 pdb=" N PRO V 39 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO V 39 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO V 39 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP i 38 " 0.013 5.00e-02 4.00e+02 1.97e-02 6.22e-01 pdb=" N PRO i 39 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO i 39 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO i 39 " 0.011 5.00e-02 4.00e+02 ... (remaining 9597 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 19970 2.35 - 2.91: 156510 2.91 - 3.48: 177827 3.48 - 4.04: 236927 4.04 - 4.60: 374491 Nonbonded interactions: 965725 Sorted by model distance: nonbonded pdb=" O LEU S 48 " pdb=" HG SER S 51 " model vdw 1.789 2.450 nonbonded pdb=" O LEU B 48 " pdb=" HG SER B 51 " model vdw 1.790 2.450 nonbonded pdb=" O LEU a 48 " pdb=" HG SER a 51 " model vdw 1.790 2.450 nonbonded pdb=" O LEU 1 48 " pdb=" HG SER 1 51 " model vdw 1.791 2.450 nonbonded pdb=" O LEU 0 48 " pdb=" HG SER 0 51 " model vdw 1.791 2.450 ... (remaining 965720 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: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } 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: 5.340 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: 0.910 Extract box with map and model: 2.190 Check model and map are aligned: 0.410 Set scattering table: 0.480 Process input model: 111.340 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.900 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: 0.020 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33840 Z= 0.159 Angle : 0.452 3.635 45840 Z= 0.247 Chirality : 0.034 0.108 4980 Planarity : 0.003 0.020 5760 Dihedral : 11.593 88.123 12780 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.13), residues: 3900 helix: 1.93 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 5.08 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 42 PHE 0.010 0.003 PHE L 63 TYR 0.002 0.001 TYR X 34 ARG 0.002 0.000 ARG Q 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1132 time to evaluate : 4.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 53 ASP cc_start: 0.6895 (t70) cc_final: 0.6657 (t70) outliers start: 0 outliers final: 0 residues processed: 1132 average time/residue: 4.1627 time to fit residues: 5301.0926 Evaluate side-chains 957 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 957 time to evaluate : 4.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 0.0020 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 326 optimal weight: 5.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 33840 Z= 0.237 Angle : 0.541 5.020 45840 Z= 0.283 Chirality : 0.037 0.108 4980 Planarity : 0.006 0.037 5760 Dihedral : 3.010 10.242 4440 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 3.82 % Allowed : 12.48 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.13), residues: 3900 helix: 2.10 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 3.10 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP z 42 PHE 0.018 0.005 PHE c 63 TYR 0.007 0.001 TYR R 34 ARG 0.006 0.000 ARG o 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 951 time to evaluate : 4.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 50 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7231 (mtp180) REVERT: o 64 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7327 (tpp) REVERT: A 50 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7240 (mtp180) REVERT: S 50 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7227 (mtp180) REVERT: r 50 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7234 (mtp180) REVERT: E 50 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7147 (mtp180) REVERT: B 25 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6500 (mm-30) REVERT: B 50 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7160 (mtp180) REVERT: i 30 MET cc_start: 0.7624 (mtm) cc_final: 0.7363 (mtm) REVERT: m 35 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5780 (mt-10) REVERT: t 50 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7107 (mtp180) REVERT: N 50 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7165 (mtp180) REVERT: J 50 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7243 (mtp180) REVERT: K 50 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7407 (mtp180) REVERT: H 50 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7221 (mtp180) REVERT: I 50 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7230 (mtp180) REVERT: u 50 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7215 (mtp180) REVERT: w 50 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7214 (mtp180) REVERT: w 64 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7222 (tpp) REVERT: y 50 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7155 (mtp180) REVERT: Y 25 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6460 (mm-30) REVERT: Y 50 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7147 (mtp180) REVERT: z 50 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7119 (mtp180) REVERT: Z 50 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7154 (mtp180) REVERT: 0 25 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6635 (mm-30) REVERT: 0 50 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7164 (mtp180) REVERT: a 50 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7114 (mtp180) REVERT: 1 50 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7222 (mtp180) REVERT: 2 25 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6619 (mm-30) REVERT: 2 50 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7104 (mtp180) REVERT: c 25 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6601 (mm-30) REVERT: c 50 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7153 (mtp180) REVERT: e 35 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5728 (mt-10) REVERT: 7 50 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7230 (mtp180) outliers start: 126 outliers final: 22 residues processed: 952 average time/residue: 4.1085 time to fit residues: 4418.8668 Evaluate side-chains 976 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 926 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain o residue 8 GLU Chi-restraints excluded: chain o residue 50 ARG Chi-restraints excluded: chain o residue 64 MET Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain q residue 31 GLN Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 64 MET Chi-restraints excluded: chain r residue 8 GLU Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain m residue 35 GLU Chi-restraints excluded: chain t residue 50 ARG Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain O residue 64 MET Chi-restraints excluded: chain V residue 31 GLN Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 50 ARG Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain u residue 50 ARG Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain v residue 31 GLN Chi-restraints excluded: chain w residue 38 ASP Chi-restraints excluded: chain w residue 50 ARG Chi-restraints excluded: chain w residue 64 MET Chi-restraints excluded: chain y residue 50 ARG Chi-restraints excluded: chain Y residue 50 ARG Chi-restraints excluded: chain z residue 31 GLN Chi-restraints excluded: chain z residue 50 ARG Chi-restraints excluded: chain Z residue 50 ARG Chi-restraints excluded: chain 0 residue 50 ARG Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain 1 residue 50 ARG Chi-restraints excluded: chain 1 residue 64 MET Chi-restraints excluded: chain b residue 31 GLN Chi-restraints excluded: chain 2 residue 50 ARG Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain c residue 50 ARG Chi-restraints excluded: chain e residue 35 GLU Chi-restraints excluded: chain 7 residue 50 ARG Chi-restraints excluded: chain 6 residue 31 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 327 optimal weight: 1.9990 chunk 353 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33840 Z= 0.221 Angle : 0.516 4.399 45840 Z= 0.271 Chirality : 0.036 0.105 4980 Planarity : 0.005 0.035 5760 Dihedral : 2.966 9.333 4440 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 3.73 % Allowed : 13.18 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.13), residues: 3900 helix: 2.15 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 2.65 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 42 PHE 0.016 0.005 PHE v 63 TYR 0.006 0.001 TYR 6 34 ARG 0.006 0.000 ARG S 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 928 time to evaluate : 4.262 Fit side-chains revert: symmetry clash REVERT: L 50 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7381 (mtp180) REVERT: o 50 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7221 (mtp180) REVERT: o 64 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7295 (tpp) REVERT: p 50 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7359 (mtp180) REVERT: A 50 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7249 (mtp180) REVERT: A 64 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7207 (tpp) REVERT: q 50 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7411 (mtp180) REVERT: S 50 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7226 (mtp180) REVERT: r 50 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7238 (mtp180) REVERT: C 50 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7394 (mtp180) REVERT: E 50 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7117 (mtp180) REVERT: B 25 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6433 (mm-30) REVERT: B 50 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7104 (mtp180) REVERT: m 35 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5728 (mt-10) REVERT: t 50 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7091 (mtp180) REVERT: N 50 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7097 (mtp180) REVERT: V 50 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7431 (mtp180) REVERT: R 50 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7414 (mtp180) REVERT: J 50 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7260 (mtp180) REVERT: H 50 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7243 (mtp180) REVERT: M 50 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7369 (mtp180) REVERT: I 50 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7246 (mtp180) REVERT: u 50 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7234 (mtp180) REVERT: v 50 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7392 (mtp180) REVERT: w 50 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7246 (mtp180) REVERT: w 64 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7269 (tpp) REVERT: W 50 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7401 (mtp180) REVERT: y 50 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7108 (mtp180) REVERT: Y 25 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6478 (mm-30) REVERT: Y 50 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7101 (mtp180) REVERT: z 50 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7094 (mtp180) REVERT: Z 25 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6445 (mm-30) REVERT: Z 50 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7091 (mtp180) REVERT: 0 25 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6501 (mm-30) REVERT: 0 50 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7083 (mtp180) REVERT: a 25 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6423 (mm-30) REVERT: a 50 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7090 (mtp180) REVERT: 1 50 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7236 (mtp180) REVERT: b 50 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7391 (mtp180) REVERT: 2 25 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6476 (mm-30) REVERT: 2 50 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7091 (mtp180) REVERT: c 50 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7106 (mtp180) REVERT: e 35 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5731 (mt-10) REVERT: 5 35 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5734 (mt-10) REVERT: 7 50 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7231 (mtp180) REVERT: 6 50 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7403 (mtp180) outliers start: 123 outliers final: 48 residues processed: 929 average time/residue: 4.2909 time to fit residues: 4482.6775 Evaluate side-chains 986 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 898 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 50 ARG Chi-restraints excluded: chain o residue 8 GLU Chi-restraints excluded: chain o residue 38 ASP Chi-restraints excluded: chain o residue 50 ARG Chi-restraints excluded: chain o residue 64 MET Chi-restraints excluded: chain p residue 31 GLN Chi-restraints excluded: chain p residue 50 ARG Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain q residue 31 GLN Chi-restraints excluded: chain q residue 50 ARG Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain S residue 38 ASP Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain S residue 64 MET Chi-restraints excluded: chain r residue 8 GLU Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain U residue 8 GLU Chi-restraints excluded: chain m residue 35 GLU Chi-restraints excluded: chain t residue 50 ARG Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 64 MET Chi-restraints excluded: chain V residue 50 ARG Chi-restraints excluded: chain P residue 8 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 50 ARG Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain v residue 31 GLN Chi-restraints excluded: chain v residue 50 ARG Chi-restraints excluded: chain w residue 50 ARG Chi-restraints excluded: chain w residue 64 MET Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 50 ARG Chi-restraints excluded: chain x residue 8 GLU Chi-restraints excluded: chain x residue 38 ASP Chi-restraints excluded: chain y residue 50 ARG Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 50 ARG Chi-restraints excluded: chain z residue 50 ARG Chi-restraints excluded: chain Z residue 50 ARG Chi-restraints excluded: chain 0 residue 31 GLN Chi-restraints excluded: chain 0 residue 50 ARG Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain 1 residue 8 GLU Chi-restraints excluded: chain 1 residue 38 ASP Chi-restraints excluded: chain 1 residue 50 ARG Chi-restraints excluded: chain 1 residue 64 MET Chi-restraints excluded: chain b residue 50 ARG Chi-restraints excluded: chain 2 residue 50 ARG Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain c residue 50 ARG Chi-restraints excluded: chain 4 residue 8 GLU Chi-restraints excluded: chain e residue 35 GLU Chi-restraints excluded: chain 5 residue 35 GLU Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain 7 residue 38 ASP Chi-restraints excluded: chain 7 residue 50 ARG Chi-restraints excluded: chain 6 residue 31 GLN Chi-restraints excluded: chain 6 residue 50 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 5.9990 chunk 246 optimal weight: 0.4980 chunk 169 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 219 optimal weight: 0.0980 chunk 328 optimal weight: 3.9990 chunk 347 optimal weight: 5.9990 chunk 171 optimal weight: 0.2980 chunk 311 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 33840 Z= 0.165 Angle : 0.463 4.120 45840 Z= 0.242 Chirality : 0.034 0.101 4980 Planarity : 0.004 0.033 5760 Dihedral : 2.816 8.489 4440 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.12 % Allowed : 13.76 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.13), residues: 3900 helix: 2.52 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 2.62 (0.53), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 42 PHE 0.014 0.004 PHE v 63 TYR 0.005 0.001 TYR C 34 ARG 0.006 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 901 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 50 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7391 (mtp180) REVERT: o 64 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7298 (tpp) REVERT: p 50 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7389 (mtp180) REVERT: q 50 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7407 (mtp180) REVERT: r 64 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7308 (tpp) REVERT: C 50 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7381 (mtp180) REVERT: B 25 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6510 (mm-30) REVERT: m 35 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5713 (mt-10) REVERT: O 50 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7162 (mtp180) REVERT: V 50 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7408 (mtp180) REVERT: R 50 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7426 (mtp180) REVERT: J 64 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7365 (tpp) REVERT: M 50 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7342 (mtp180) REVERT: v 50 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7394 (mtp180) REVERT: w 64 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7205 (tpp) REVERT: W 50 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7391 (mtp180) REVERT: b 50 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7381 (mtp180) REVERT: e 35 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5723 (mt-10) REVERT: 7 64 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7348 (tpp) REVERT: 6 50 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7394 (mtp180) outliers start: 136 outliers final: 41 residues processed: 902 average time/residue: 4.3868 time to fit residues: 4419.2874 Evaluate side-chains 953 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 893 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 50 ARG Chi-restraints excluded: chain o residue 38 ASP Chi-restraints excluded: chain o residue 64 MET Chi-restraints excluded: chain p residue 31 GLN Chi-restraints excluded: chain p residue 50 ARG Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain q residue 31 GLN Chi-restraints excluded: chain q residue 50 ARG Chi-restraints excluded: chain r residue 38 ASP Chi-restraints excluded: chain r residue 64 MET Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain U residue 38 ASP Chi-restraints excluded: chain m residue 35 GLU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain t residue 64 MET Chi-restraints excluded: chain N residue 64 MET Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 64 MET Chi-restraints excluded: chain V residue 31 GLN Chi-restraints excluded: chain V residue 50 ARG Chi-restraints excluded: chain P residue 38 ASP Chi-restraints excluded: chain j residue 8 GLU Chi-restraints excluded: chain j residue 38 ASP Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain n residue 31 GLN Chi-restraints excluded: chain h residue 38 ASP Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain u residue 38 ASP Chi-restraints excluded: chain v residue 50 ARG Chi-restraints excluded: chain w residue 8 GLU Chi-restraints excluded: chain w residue 64 MET Chi-restraints excluded: chain W residue 50 ARG Chi-restraints excluded: chain x residue 38 ASP Chi-restraints excluded: chain y residue 64 MET Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain z residue 64 MET Chi-restraints excluded: chain 0 residue 31 GLN Chi-restraints excluded: chain 1 residue 38 ASP Chi-restraints excluded: chain b residue 50 ARG Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain 4 residue 38 ASP Chi-restraints excluded: chain e residue 35 GLU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain 7 residue 64 MET Chi-restraints excluded: chain 6 residue 50 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 312 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 33840 Z= 0.257 Angle : 0.555 5.033 45840 Z= 0.294 Chirality : 0.038 0.109 4980 Planarity : 0.006 0.040 5760 Dihedral : 3.119 9.597 4440 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 4.42 % Allowed : 15.55 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.13), residues: 3900 helix: 2.07 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 2.62 (0.55), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 42 PHE 0.016 0.006 PHE L 63 TYR 0.007 0.001 TYR 6 34 ARG 0.007 0.000 ARG I 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 929 time to evaluate : 4.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 50 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7499 (mtp180) REVERT: o 50 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7201 (mtp180) REVERT: o 64 MET cc_start: 0.7544 (mtp) cc_final: 0.7250 (tpp) REVERT: p 50 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7495 (mtp180) REVERT: A 50 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7241 (mtp180) REVERT: q 50 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7494 (mtp180) REVERT: S 50 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7210 (mtp180) REVERT: r 50 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7210 (mtp180) REVERT: r 64 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7277 (tpp) REVERT: C 50 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7509 (mtp180) REVERT: D 50 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7499 (mtp180) REVERT: E 50 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7337 (mtp180) REVERT: B 25 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6486 (mm-30) REVERT: m 35 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5766 (mt-10) REVERT: t 25 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6625 (mm-30) REVERT: N 25 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6604 (mm-30) REVERT: N 50 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7320 (mtp180) REVERT: O 50 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7241 (mtp180) REVERT: V 50 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7504 (mtp180) REVERT: R 50 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7536 (mtp180) REVERT: J 50 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7218 (mtp180) REVERT: K 50 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7342 (mtp180) REVERT: H 50 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7212 (mtp180) REVERT: M 50 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7481 (mtp180) REVERT: I 50 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7222 (mtp180) REVERT: I 64 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7293 (tpp) REVERT: u 50 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7221 (mtp180) REVERT: u 64 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7248 (tpp) REVERT: v 50 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7523 (mtp180) REVERT: w 50 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7218 (mtp180) REVERT: w 64 MET cc_start: 0.7540 (mtp) cc_final: 0.7246 (tpp) REVERT: W 50 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7497 (mtp180) REVERT: X 35 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5773 (mt-10) REVERT: y 25 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6435 (mm-30) REVERT: Y 25 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6434 (mm-30) REVERT: Y 50 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7326 (mtp180) REVERT: Z 25 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6456 (mm-30) REVERT: Z 50 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7340 (mtp180) REVERT: 0 50 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7320 (mtp180) REVERT: a 25 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6407 (mm-30) REVERT: a 50 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7321 (mtp180) REVERT: 1 50 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7218 (mtp180) REVERT: 1 64 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7278 (tpp) REVERT: b 50 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7491 (mtp180) REVERT: 2 25 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6425 (mm-30) REVERT: e 35 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5776 (mt-10) REVERT: 7 50 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7209 (mtp180) REVERT: 6 50 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7486 (mtp180) outliers start: 146 outliers final: 60 residues processed: 930 average time/residue: 4.2539 time to fit residues: 4420.7378 Evaluate side-chains 1009 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 911 time to evaluate : 4.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 50 ARG Chi-restraints excluded: chain o residue 8 GLU Chi-restraints excluded: chain o residue 50 ARG Chi-restraints excluded: chain p residue 31 GLN Chi-restraints excluded: chain p residue 50 ARG Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain q residue 31 GLN Chi-restraints excluded: chain q residue 50 ARG Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain r residue 8 GLU Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 64 MET Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain U residue 38 ASP Chi-restraints excluded: chain m residue 35 GLU Chi-restraints excluded: chain g residue 31 GLN Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain t residue 8 GLU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 64 MET Chi-restraints excluded: chain V residue 31 GLN Chi-restraints excluded: chain V residue 50 ARG Chi-restraints excluded: chain P residue 31 GLN Chi-restraints excluded: chain P residue 38 ASP Chi-restraints excluded: chain j residue 8 GLU Chi-restraints excluded: chain j residue 38 ASP Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain h residue 38 ASP Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 50 ARG Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 50 ARG Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain v residue 50 ARG Chi-restraints excluded: chain w residue 8 GLU Chi-restraints excluded: chain w residue 50 ARG Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 50 ARG Chi-restraints excluded: chain x residue 38 ASP Chi-restraints excluded: chain X residue 35 GLU Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 50 ARG Chi-restraints excluded: chain z residue 8 GLU Chi-restraints excluded: chain z residue 31 GLN Chi-restraints excluded: chain Z residue 8 GLU Chi-restraints excluded: chain Z residue 50 ARG Chi-restraints excluded: chain 0 residue 8 GLU Chi-restraints excluded: chain 0 residue 31 GLN Chi-restraints excluded: chain 0 residue 50 ARG Chi-restraints excluded: chain a residue 8 GLU Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain 1 residue 8 GLU Chi-restraints excluded: chain 1 residue 50 ARG Chi-restraints excluded: chain 1 residue 64 MET Chi-restraints excluded: chain b residue 31 GLN Chi-restraints excluded: chain b residue 50 ARG Chi-restraints excluded: chain 2 residue 8 GLU Chi-restraints excluded: chain 2 residue 31 GLN Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain 4 residue 38 ASP Chi-restraints excluded: chain e residue 35 GLU Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain 7 residue 50 ARG Chi-restraints excluded: chain 6 residue 50 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 4.9990 chunk 313 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 348 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 33840 Z= 0.243 Angle : 0.537 4.374 45840 Z= 0.286 Chirality : 0.037 0.106 4980 Planarity : 0.006 0.042 5760 Dihedral : 3.115 9.805 4440 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.97 % Allowed : 16.82 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.13), residues: 3900 helix: 2.05 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 2.67 (0.56), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 42 PHE 0.016 0.006 PHE p 63 TYR 0.007 0.001 TYR v 34 ARG 0.005 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 922 time to evaluate : 4.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 50 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7540 (mtp180) REVERT: o 50 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7212 (mtp180) REVERT: o 64 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7269 (tpp) REVERT: p 50 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7533 (mtp180) REVERT: A 50 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7239 (mtp180) REVERT: S 50 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7206 (mtp180) REVERT: r 50 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7246 (mtp180) REVERT: r 64 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7294 (tpp) REVERT: B 25 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6462 (mm-30) REVERT: m 35 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5764 (mt-10) REVERT: t 25 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6624 (mm-30) REVERT: t 35 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5690 (mt-10) REVERT: N 25 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6642 (mm-30) REVERT: O 50 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7218 (mtp180) REVERT: Q 35 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5776 (mt-10) REVERT: J 50 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7215 (mtp180) REVERT: K 50 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7333 (mtp180) REVERT: H 50 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7204 (mtp180) REVERT: M 50 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7516 (mtp180) REVERT: I 50 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7258 (mtp180) REVERT: I 64 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7297 (tpp) REVERT: u 50 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7235 (mtp180) REVERT: u 64 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7240 (tpp) REVERT: w 50 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7208 (mtp180) REVERT: w 64 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7260 (tpp) REVERT: W 50 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7543 (mtp180) REVERT: X 35 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5766 (mt-10) REVERT: y 25 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6358 (mm-30) REVERT: Y 25 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6432 (mm-30) REVERT: Z 25 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6471 (mm-30) REVERT: 0 25 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6549 (mm-30) REVERT: a 25 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6473 (mm-30) REVERT: 1 50 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7198 (mtp180) REVERT: 1 64 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7265 (tpp) REVERT: b 50 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7533 (mtp180) REVERT: 2 25 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6403 (mm-30) REVERT: e 35 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5732 (mt-10) REVERT: 5 35 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5722 (mt-10) REVERT: 7 50 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7190 (mtp180) outliers start: 131 outliers final: 58 residues processed: 923 average time/residue: 4.2794 time to fit residues: 4409.2049 Evaluate side-chains 997 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 907 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 50 ARG Chi-restraints excluded: chain o residue 8 GLU Chi-restraints excluded: chain o residue 50 ARG Chi-restraints excluded: chain o residue 64 MET Chi-restraints excluded: chain p residue 50 ARG Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain q residue 31 GLN Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain r residue 8 GLU Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 64 MET Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain U residue 38 ASP Chi-restraints excluded: chain m residue 35 GLU Chi-restraints excluded: chain g residue 31 GLN Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain t residue 8 GLU Chi-restraints excluded: chain t residue 35 GLU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 64 MET Chi-restraints excluded: chain P residue 38 ASP Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain j residue 8 GLU Chi-restraints excluded: chain j residue 38 ASP Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 38 ASP Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 50 ARG Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 50 ARG Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain v residue 31 GLN Chi-restraints excluded: chain w residue 8 GLU Chi-restraints excluded: chain w residue 50 ARG Chi-restraints excluded: chain w residue 64 MET Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 50 ARG Chi-restraints excluded: chain x residue 38 ASP Chi-restraints excluded: chain X residue 35 GLU Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain z residue 31 GLN Chi-restraints excluded: chain Z residue 8 GLU Chi-restraints excluded: chain 0 residue 8 GLU Chi-restraints excluded: chain 0 residue 25 GLU Chi-restraints excluded: chain 0 residue 31 GLN Chi-restraints excluded: chain a residue 8 GLU Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain 1 residue 8 GLU Chi-restraints excluded: chain 1 residue 50 ARG Chi-restraints excluded: chain 1 residue 64 MET Chi-restraints excluded: chain b residue 31 GLN Chi-restraints excluded: chain b residue 50 ARG Chi-restraints excluded: chain 2 residue 31 GLN Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain 4 residue 31 GLN Chi-restraints excluded: chain 4 residue 38 ASP Chi-restraints excluded: chain e residue 35 GLU Chi-restraints excluded: chain 5 residue 35 GLU Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain 7 residue 50 ARG Chi-restraints excluded: chain 6 residue 31 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 33840 Z= 0.315 Angle : 0.608 4.560 45840 Z= 0.326 Chirality : 0.041 0.112 4980 Planarity : 0.007 0.068 5760 Dihedral : 3.372 10.468 4440 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.79 % Allowed : 16.94 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.13), residues: 3900 helix: 1.70 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 2.57 (0.57), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP t 42 PHE 0.018 0.007 PHE v 63 TYR 0.007 0.001 TYR R 34 ARG 0.008 0.001 ARG z 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 913 time to evaluate : 4.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 50 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7218 (mtp180) REVERT: o 64 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7240 (tpp) REVERT: p 50 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7540 (mtp180) REVERT: A 50 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7259 (mtp180) REVERT: S 50 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7226 (mtp180) REVERT: r 50 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7388 (mtp180) REVERT: r 64 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7312 (tpp) REVERT: E 25 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6559 (mm-30) REVERT: B 25 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6499 (mm-30) REVERT: m 35 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5788 (mt-10) REVERT: t 25 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6589 (mm-30) REVERT: t 35 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5682 (mt-10) REVERT: N 25 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6602 (mm-30) REVERT: O 50 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7244 (mtp180) REVERT: Q 35 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5769 (mt-10) REVERT: J 50 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7240 (mtp180) REVERT: K 50 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7496 (mtp180) REVERT: H 50 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7418 (mtp180) REVERT: M 50 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7538 (mtp180) REVERT: I 50 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7424 (mtp180) REVERT: I 64 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7258 (tpp) REVERT: u 50 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7391 (mtp180) REVERT: u 64 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7237 (tpp) REVERT: w 50 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7374 (mtp180) REVERT: w 64 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7244 (tpp) REVERT: X 35 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5749 (mt-10) REVERT: y 25 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6412 (mm-30) REVERT: Y 25 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6470 (mm-30) REVERT: z 25 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6540 (mm-30) REVERT: Z 25 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6436 (mm-30) REVERT: 0 25 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6552 (mm-30) REVERT: a 25 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6493 (mm-30) REVERT: 1 50 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7226 (mtp180) REVERT: 1 64 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7235 (tpp) REVERT: 2 25 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6411 (mm-30) REVERT: e 35 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5786 (mt-10) REVERT: 5 35 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5731 (mt-10) REVERT: 7 50 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7212 (mtp180) outliers start: 125 outliers final: 68 residues processed: 914 average time/residue: 4.2431 time to fit residues: 4332.4698 Evaluate side-chains 994 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 898 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain o residue 8 GLU Chi-restraints excluded: chain o residue 50 ARG Chi-restraints excluded: chain o residue 64 MET Chi-restraints excluded: chain p residue 31 GLN Chi-restraints excluded: chain p residue 50 ARG Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain q residue 31 GLN Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain r residue 8 GLU Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 64 MET Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 38 ASP Chi-restraints excluded: chain m residue 35 GLU Chi-restraints excluded: chain g residue 31 GLN Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain t residue 8 GLU Chi-restraints excluded: chain t residue 31 GLN Chi-restraints excluded: chain t residue 35 GLU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 64 MET Chi-restraints excluded: chain P residue 31 GLN Chi-restraints excluded: chain P residue 38 ASP Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain j residue 8 GLU Chi-restraints excluded: chain j residue 38 ASP Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 38 ASP Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 50 ARG Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 50 ARG Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain w residue 8 GLU Chi-restraints excluded: chain w residue 50 ARG Chi-restraints excluded: chain w residue 64 MET Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain x residue 31 GLN Chi-restraints excluded: chain x residue 38 ASP Chi-restraints excluded: chain X residue 35 GLU Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain z residue 8 GLU Chi-restraints excluded: chain z residue 31 GLN Chi-restraints excluded: chain Z residue 8 GLU Chi-restraints excluded: chain 0 residue 8 GLU Chi-restraints excluded: chain 0 residue 31 GLN Chi-restraints excluded: chain a residue 8 GLU Chi-restraints excluded: chain a residue 31 GLN Chi-restraints excluded: chain 1 residue 8 GLU Chi-restraints excluded: chain 1 residue 50 ARG Chi-restraints excluded: chain 1 residue 64 MET Chi-restraints excluded: chain b residue 31 GLN Chi-restraints excluded: chain 2 residue 8 GLU Chi-restraints excluded: chain 2 residue 31 GLN Chi-restraints excluded: chain c residue 8 GLU Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain 4 residue 31 GLN Chi-restraints excluded: chain 4 residue 38 ASP Chi-restraints excluded: chain e residue 35 GLU Chi-restraints excluded: chain 5 residue 35 GLU Chi-restraints excluded: chain f residue 8 GLU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain 7 residue 38 ASP Chi-restraints excluded: chain 7 residue 50 ARG Chi-restraints excluded: chain 6 residue 31 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 220 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 33840 Z= 0.155 Angle : 0.467 4.237 45840 Z= 0.246 Chirality : 0.033 0.099 4980 Planarity : 0.005 0.067 5760 Dihedral : 2.933 9.145 4440 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 2.67 % Allowed : 17.85 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.13), residues: 3900 helix: 2.50 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 2.93 (0.59), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP t 42 PHE 0.014 0.004 PHE V 63 TYR 0.004 0.001 TYR K 34 ARG 0.009 0.000 ARG Z 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 894 time to evaluate : 4.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 50 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7149 (mtp180) REVERT: o 64 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7188 (tpp) REVERT: A 50 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7164 (mtp180) REVERT: S 50 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7150 (mtp180) REVERT: r 50 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7153 (mtp180) REVERT: r 64 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7303 (tpp) REVERT: B 25 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6446 (mm-30) REVERT: t 35 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5685 (mt-10) REVERT: O 50 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7110 (mtp180) REVERT: O 64 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7262 (tpp) REVERT: Q 35 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5801 (mt-10) REVERT: J 50 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7159 (mtp180) REVERT: H 50 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7150 (mtp180) REVERT: I 50 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7165 (mtp180) REVERT: I 64 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7375 (tpp) REVERT: u 50 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7159 (mtp180) REVERT: u 64 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7227 (tpp) REVERT: w 50 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7156 (mtp180) REVERT: w 64 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7257 (tpp) REVERT: X 35 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5814 (mt-10) REVERT: 1 50 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7147 (mtp180) REVERT: 1 64 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7236 (tpp) REVERT: 2 25 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6411 (mm-30) REVERT: 5 35 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5761 (mt-10) REVERT: 7 50 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7134 (mtp180) outliers start: 88 outliers final: 38 residues processed: 895 average time/residue: 4.4013 time to fit residues: 4386.3456 Evaluate side-chains 952 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 891 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 50 ARG Chi-restraints excluded: chain o residue 64 MET Chi-restraints excluded: chain p residue 31 GLN Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain q residue 31 GLN Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 64 MET Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain U residue 38 ASP Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain t residue 31 GLN Chi-restraints excluded: chain t residue 35 GLU Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 64 MET Chi-restraints excluded: chain V residue 31 GLN Chi-restraints excluded: chain P residue 38 ASP Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain j residue 38 ASP Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain h residue 38 ASP Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 50 ARG Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain w residue 8 GLU Chi-restraints excluded: chain w residue 50 ARG Chi-restraints excluded: chain w residue 64 MET Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain x residue 38 ASP Chi-restraints excluded: chain X residue 35 GLU Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain z residue 31 GLN Chi-restraints excluded: chain 0 residue 31 GLN Chi-restraints excluded: chain 1 residue 31 GLN Chi-restraints excluded: chain 1 residue 50 ARG Chi-restraints excluded: chain 1 residue 64 MET Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain 4 residue 31 GLN Chi-restraints excluded: chain 4 residue 38 ASP Chi-restraints excluded: chain 5 residue 35 GLU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain 7 residue 31 GLN Chi-restraints excluded: chain 7 residue 38 ASP Chi-restraints excluded: chain 7 residue 50 ARG Chi-restraints excluded: chain 6 residue 31 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 303 optimal weight: 0.3980 chunk 323 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 253 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 33840 Z= 0.238 Angle : 0.548 4.427 45840 Z= 0.292 Chirality : 0.037 0.105 4980 Planarity : 0.006 0.067 5760 Dihedral : 3.178 10.318 4440 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.67 % Allowed : 17.79 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.13), residues: 3900 helix: 2.13 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 2.95 (0.60), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 42 PHE 0.016 0.005 PHE C 63 TYR 0.007 0.001 TYR p 34 ARG 0.009 0.001 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 919 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 50 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7349 (mtp180) REVERT: o 64 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7258 (tpp) REVERT: A 50 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7378 (mtp180) REVERT: S 50 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7346 (mtp180) REVERT: r 50 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7386 (mtp180) REVERT: r 64 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7313 (tpp) REVERT: B 25 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6457 (mm-30) REVERT: t 35 GLU cc_start: 0.6053 (OUTLIER) cc_final: 0.5691 (mt-10) REVERT: N 25 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6658 (mm-30) REVERT: O 50 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7221 (mtp180) REVERT: Q 35 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5790 (mt-10) REVERT: J 50 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7391 (mtp180) REVERT: H 50 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7355 (mtp180) REVERT: I 50 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7366 (mtp180) REVERT: I 64 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7308 (tpp) REVERT: u 50 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7374 (mtp180) REVERT: u 64 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7248 (tpp) REVERT: w 50 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7392 (mtp180) REVERT: w 64 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7247 (tpp) REVERT: X 35 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5775 (mt-10) REVERT: y 25 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6416 (mm-30) REVERT: Y 25 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6445 (mm-30) REVERT: Z 25 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6447 (mm-30) REVERT: 0 25 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6610 (mm-30) REVERT: a 25 GLU cc_start: 0.6688 (mm-30) cc_final: 0.6362 (mm-30) REVERT: 1 50 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7354 (mtp180) REVERT: 1 64 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7265 (tpp) REVERT: 2 25 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6414 (mm-30) REVERT: 5 35 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5737 (mt-10) REVERT: 7 50 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7341 (mtp180) outliers start: 88 outliers final: 47 residues processed: 920 average time/residue: 4.2778 time to fit residues: 4400.4089 Evaluate side-chains 981 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 911 time to evaluate : 4.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain o residue 50 ARG Chi-restraints excluded: chain o residue 64 MET Chi-restraints excluded: chain p residue 31 GLN Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain q residue 31 GLN Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain r residue 8 GLU Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 64 MET Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain U residue 38 ASP Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain t residue 31 GLN Chi-restraints excluded: chain t residue 35 GLU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 64 MET Chi-restraints excluded: chain V residue 31 GLN Chi-restraints excluded: chain P residue 31 GLN Chi-restraints excluded: chain P residue 38 ASP Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain j residue 38 ASP Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 38 ASP Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 50 ARG Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain w residue 8 GLU Chi-restraints excluded: chain w residue 50 ARG Chi-restraints excluded: chain w residue 64 MET Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain x residue 38 ASP Chi-restraints excluded: chain X residue 35 GLU Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain z residue 31 GLN Chi-restraints excluded: chain 0 residue 31 GLN Chi-restraints excluded: chain 1 residue 8 GLU Chi-restraints excluded: chain 1 residue 50 ARG Chi-restraints excluded: chain 1 residue 64 MET Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain 4 residue 31 GLN Chi-restraints excluded: chain 4 residue 38 ASP Chi-restraints excluded: chain 5 residue 35 GLU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain 7 residue 50 ARG Chi-restraints excluded: chain 6 residue 31 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 4.9990 chunk 341 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 237 optimal weight: 0.8980 chunk 358 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 33840 Z= 0.147 Angle : 0.458 4.167 45840 Z= 0.242 Chirality : 0.033 0.101 4980 Planarity : 0.005 0.063 5760 Dihedral : 2.851 9.054 4440 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.85 % Allowed : 18.55 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.13), residues: 3900 helix: 2.70 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 3.13 (0.61), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 42 PHE 0.012 0.004 PHE V 63 TYR 0.004 0.001 TYR M 34 ARG 0.009 0.000 ARG y 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 907 time to evaluate : 4.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 50 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7112 (mtp180) REVERT: o 64 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7284 (tpp) REVERT: A 50 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7121 (mtp180) REVERT: S 50 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7116 (mtp180) REVERT: r 50 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7141 (mtp180) REVERT: r 64 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7259 (tpp) REVERT: t 35 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5673 (mt-10) REVERT: O 50 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7105 (mtp180) REVERT: O 64 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7233 (tpp) REVERT: Q 35 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5786 (mt-10) REVERT: J 50 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7150 (mtp180) REVERT: H 50 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7121 (mtp180) REVERT: I 50 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7147 (mtp180) REVERT: I 64 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7313 (tpp) REVERT: u 50 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7123 (mtp180) REVERT: u 64 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7259 (tpp) REVERT: w 50 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7131 (mtp180) REVERT: w 64 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7264 (tpp) REVERT: X 35 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5781 (mt-10) REVERT: 1 50 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7124 (mtp180) REVERT: 1 64 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7242 (tpp) REVERT: 5 35 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5712 (mt-10) REVERT: 7 50 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7115 (mtp180) outliers start: 61 outliers final: 30 residues processed: 908 average time/residue: 4.4190 time to fit residues: 4498.7748 Evaluate side-chains 960 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 907 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 50 ARG Chi-restraints excluded: chain o residue 64 MET Chi-restraints excluded: chain p residue 31 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain q residue 31 GLN Chi-restraints excluded: chain S residue 50 ARG Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 64 MET Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain t residue 31 GLN Chi-restraints excluded: chain t residue 35 GLU Chi-restraints excluded: chain O residue 50 ARG Chi-restraints excluded: chain O residue 64 MET Chi-restraints excluded: chain P residue 8 GLU Chi-restraints excluded: chain P residue 38 ASP Chi-restraints excluded: chain Q residue 35 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 38 ASP Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain u residue 50 ARG Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain w residue 50 ARG Chi-restraints excluded: chain w residue 64 MET Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain x residue 38 ASP Chi-restraints excluded: chain X residue 35 GLU Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain z residue 31 GLN Chi-restraints excluded: chain 0 residue 31 GLN Chi-restraints excluded: chain 1 residue 31 GLN Chi-restraints excluded: chain 1 residue 50 ARG Chi-restraints excluded: chain 1 residue 64 MET Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain 4 residue 38 ASP Chi-restraints excluded: chain 5 residue 35 GLU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain 7 residue 31 GLN Chi-restraints excluded: chain 7 residue 50 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 263 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.191445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176021 restraints weight = 93357.292| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.10 r_work: 0.3902 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 33840 Z= 0.192 Angle : 0.509 4.346 45840 Z= 0.271 Chirality : 0.035 0.103 4980 Planarity : 0.006 0.062 5760 Dihedral : 3.027 10.251 4440 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.91 % Allowed : 19.61 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.13), residues: 3900 helix: 2.49 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 2.97 (0.61), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP t 42 PHE 0.014 0.005 PHE g 63 TYR 0.006 0.001 TYR R 34 ARG 0.008 0.001 ARG I 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50044.36 seconds wall clock time: 847 minutes 38.36 seconds (50858.36 seconds total)