Starting phenix.real_space_refine on Sat Jan 20 07:48:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f54_28860/01_2024/8f54_28860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f54_28860/01_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f54_28860/01_2024/8f54_28860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f54_28860/01_2024/8f54_28860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f54_28860/01_2024/8f54_28860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f54_28860/01_2024/8f54_28860.pdb" } 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 Residue "c PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 21.33, per 1000 atoms: 0.32 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.16 Conformation dependent library (CDL) restraints added in 5.1 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: 3.70 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: 23.16 Time building geometry restraints manager: 44.58 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: 100.68 - 107.34: 2370 107.34 - 114.01: 80149 114.01 - 120.67: 24299 120.67 - 127.33: 15642 127.33 - 133.99: 600 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: 28805 17.62 - 35.25: 1202 35.25 - 52.87: 333 52.87 - 70.50: 105 70.50 - 88.12: 35 Dihedral angle restraints: 30480 sinusoidal: 16800 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 30477 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 1.850 nonbonded pdb=" O LEU B 48 " pdb=" HG SER B 51 " model vdw 1.790 1.850 nonbonded pdb=" O LEU a 48 " pdb=" HG SER a 51 " model vdw 1.790 1.850 nonbonded pdb=" O LEU 1 48 " pdb=" HG SER 1 51 " model vdw 1.791 1.850 nonbonded pdb=" O LEU 0 48 " pdb=" HG SER 0 51 " model vdw 1.791 1.850 ... (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 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.710 Extract box with map and model: 11.840 Check model and map are aligned: 0.730 Set scattering table: 0.460 Process input model: 167.060 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.750 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:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.050 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 1132 time to evaluate : 4.090 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: 4.0153 time to fit residues: 5113.3627 Evaluate side-chains 957 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 957 time to evaluate : 4.102 ------------------------------------------------------------------------------- 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: 0.0010 chunk 184 optimal weight: 3.9990 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: 2.9994 ------------------------------------------------------------------------------- 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: 0.7548 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 33840 Z= 0.250 Angle : 0.544 4.995 45840 Z= 0.285 Chirality : 0.038 0.108 4980 Planarity : 0.006 0.036 5760 Dihedral : 3.054 10.430 4440 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 3.79 % Allowed : 12.58 % Favored : 83.64 % 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: 3.15 (0.13), residues: 3900 helix: 2.06 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : 3.20 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP z 42 PHE 0.018 0.006 PHE c 63 TYR 0.007 0.001 TYR R 34 ARG 0.005 0.000 ARG H 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 1070 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 945 time to evaluate : 4.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 50 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7220 (mtp180) REVERT: o 64 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7335 (tpp) REVERT: A 50 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7219 (mtp180) REVERT: S 50 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7242 (mtp180) REVERT: r 50 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7235 (mtp180) REVERT: E 50 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7162 (mtp180) REVERT: B 25 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6602 (mm-30) REVERT: B 50 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7157 (mtp180) REVERT: m 35 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5761 (mt-10) REVERT: t 50 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7113 (mtp180) REVERT: N 50 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7181 (mtp180) REVERT: J 50 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7244 (mtp180) REVERT: K 50 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7379 (mtp180) REVERT: H 50 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7228 (mtp180) REVERT: I 50 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7209 (mtp180) REVERT: u 50 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7216 (mtp180) REVERT: w 50 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7200 (mtp180) REVERT: w 64 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7320 (tpp) REVERT: y 50 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7159 (mtp180) REVERT: Y 50 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7156 (mtp180) REVERT: z 50 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7116 (mtp180) REVERT: Z 50 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7148 (mtp180) REVERT: 0 50 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7164 (mtp180) REVERT: a 50 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7120 (mtp180) REVERT: 1 50 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7222 (mtp180) REVERT: 2 50 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7092 (mtp180) REVERT: c 50 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7161 (mtp180) REVERT: e 35 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.5737 (mt-10) REVERT: 7 50 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7207 (mtp180) outliers start: 125 outliers final: 24 residues processed: 946 average time/residue: 3.7879 time to fit residues: 4034.2268 Evaluate side-chains 972 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 920 time to evaluate : 3.292 ------------------------------------------------------------------------------- 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 A residue 64 MET 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 D residue 31 GLN 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 50 ARG Chi-restraints excluded: chain w residue 64 MET Chi-restraints excluded: chain W residue 31 GLN 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: 5.9990 chunk 272 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 327 optimal weight: 4.9990 chunk 353 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: