Starting phenix.real_space_refine (version: 1.19rc7) on Wed Jan 6 11:34:20 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/01_2021/7jsv_22460_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/01_2021/7jsv_22460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/01_2021/7jsv_22460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/01_2021/7jsv_22460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/01_2021/7jsv_22460_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/01_2021/7jsv_22460_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 22140 Number of models: 1 Model: "" Number of chains: 82 Chain: "A" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "B" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "C" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "E" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "F" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "G" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "H" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "I" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "J" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "K" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "L" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "M" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "N" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "O" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "P" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "Q" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "R" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "S" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "T" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "U" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "V" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "W" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "X" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "Y" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "Z" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "a" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "b" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "c" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "d" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "e" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "f" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "g" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "h" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "i" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "j" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "k" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "l" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "m" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "n" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "o" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.62, per 1000 atoms: 0.52 Found NCS groups: ncs_group { reference = 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' } Number of scatterers: 22140 At special positions: 0 Unit cell: (98.28, 98.28, 170.64, 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 205 16.00 P 41 15.00 O 4018 8.00 N 3075 7.00 C 14801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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: 9.16 Conformation dependent library (CDL) restraints added in 3.0 seconds 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS A 16 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 44 Processing helix chain 'A' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY A 52 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 57 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 64 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS B 16 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 44 Processing helix chain 'B' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY B 52 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 57 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 64 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS C 16 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 44 Processing helix chain 'C' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY C 52 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 57 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET C 64 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS D 16 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 44 Processing helix chain 'D' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY D 52 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 57 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D 64 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS E 16 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE E 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 44 Processing helix chain 'E' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY E 52 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET E 64 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS F 16 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 44 Processing helix chain 'F' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY F 52 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 57 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET F 64 " --> pdb=" O THR F 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS G 16 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE G 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 44 Processing helix chain 'G' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY G 52 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER G 57 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET G 64 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS H 16 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE H 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 44 Processing helix chain 'H' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY H 52 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER H 57 " --> pdb=" O ALA H 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET H 64 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS I 16 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE I 19 " --> pdb=" O LYS I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 44 Processing helix chain 'I' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY I 52 " --> pdb=" O PHE I 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER I 57 " --> pdb=" O ALA I 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET I 64 " --> pdb=" O THR I 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS J 16 " --> pdb=" O ALA J 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE J 19 " --> pdb=" O LYS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 44 Processing helix chain 'J' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY J 52 " --> pdb=" O PHE J 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER J 57 " --> pdb=" O ALA J 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET J 64 " --> pdb=" O THR J 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS K 16 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE K 19 " --> pdb=" O LYS K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 44 Processing helix chain 'K' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY K 52 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER K 57 " --> pdb=" O ALA K 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET K 64 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS L 16 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE L 19 " --> pdb=" O LYS L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 44 Processing helix chain 'L' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY L 52 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER L 57 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET L 64 " --> pdb=" O THR L 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS M 16 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE M 19 " --> pdb=" O LYS M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 44 Processing helix chain 'M' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY M 52 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER M 57 " --> pdb=" O ALA M 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET M 64 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS N 16 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE N 19 " --> pdb=" O LYS N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 44 Processing helix chain 'N' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY N 52 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER N 57 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET N 64 " --> pdb=" O THR N 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS O 16 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE O 19 " --> pdb=" O LYS O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 44 Processing helix chain 'O' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY O 52 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER O 57 " --> pdb=" O ALA O 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET O 64 " --> pdb=" O THR O 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS P 16 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE P 19 " --> pdb=" O LYS P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 44 Processing helix chain 'P' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY P 52 " --> pdb=" O PHE P 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER P 57 " --> pdb=" O ALA P 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET P 64 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS Q 16 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE Q 19 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 44 Processing helix chain 'Q' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY Q 52 " --> pdb=" O PHE Q 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER Q 57 " --> pdb=" O ALA Q 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET Q 64 " --> pdb=" O THR Q 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS R 16 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE R 19 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 44 Processing helix chain 'R' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY R 52 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER R 57 " --> pdb=" O ALA R 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET R 64 " --> pdb=" O THR R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS S 16 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE S 19 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 44 Processing helix chain 'S' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY S 52 " --> pdb=" O PHE S 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER S 57 " --> pdb=" O ALA S 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET S 64 " --> pdb=" O THR S 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS T 16 " --> pdb=" O ALA T 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE T 19 " --> pdb=" O LYS T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 24 through 44 Processing helix chain 'T' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY T 52 " --> pdb=" O PHE T 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER T 57 " --> pdb=" O ALA T 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET T 64 " --> pdb=" O THR T 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS U 16 " --> pdb=" O ALA U 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE U 19 " --> pdb=" O LYS U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 44 Processing helix chain 'U' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY U 52 " --> pdb=" O PHE U 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER U 57 " --> pdb=" O ALA U 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET U 64 " --> pdb=" O THR U 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS V 16 " --> pdb=" O ALA V 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE V 19 " --> pdb=" O LYS V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 24 through 44 Processing helix chain 'V' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY V 52 " --> pdb=" O PHE V 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET V 64 " --> pdb=" O THR V 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS W 16 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE W 19 " --> pdb=" O LYS W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 44 Processing helix chain 'W' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY W 52 " --> pdb=" O PHE W 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER W 57 " --> pdb=" O ALA W 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET W 64 " --> pdb=" O THR W 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE X 19 " --> pdb=" O LYS X 16 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 44 Processing helix chain 'X' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY X 52 " --> pdb=" O PHE X 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER X 57 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET X 64 " --> pdb=" O THR X 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS Y 16 " --> pdb=" O ALA Y 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE Y 19 " --> pdb=" O LYS Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 44 Processing helix chain 'Y' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY Y 52 " --> pdb=" O PHE Y 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER Y 57 " --> pdb=" O ALA Y 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET Y 64 " --> pdb=" O THR Y 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS Z 16 " --> pdb=" O ALA Z 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE Z 19 " --> pdb=" O LYS Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 44 Processing helix chain 'Z' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY Z 52 " --> pdb=" O PHE Z 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER Z 57 " --> pdb=" O ALA Z 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET Z 64 " --> pdb=" O THR Z 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS a 16 " --> pdb=" O ALA a 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE a 19 " --> pdb=" O LYS a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 24 through 44 Processing helix chain 'a' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY a 52 " --> pdb=" O PHE a 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER a 57 " --> pdb=" O ALA a 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET a 64 " --> pdb=" O THR a 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS b 16 " --> pdb=" O ALA b 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE b 19 " --> pdb=" O LYS b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY b 52 " --> pdb=" O PHE b 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER b 57 " --> pdb=" O ALA b 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET b 64 " --> pdb=" O THR b 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS c 16 " --> pdb=" O ALA c 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE c 19 " --> pdb=" O LYS c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 44 Processing helix chain 'c' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY c 52 " --> pdb=" O PHE c 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER c 57 " --> pdb=" O ALA c 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET c 64 " --> pdb=" O THR c 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS d 16 " --> pdb=" O ALA d 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE d 19 " --> pdb=" O LYS d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 44 Processing helix chain 'd' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY d 52 " --> pdb=" O PHE d 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER d 57 " --> pdb=" O ALA d 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET d 64 " --> pdb=" O THR d 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS e 16 " --> pdb=" O ALA e 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE e 19 " --> pdb=" O LYS e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 24 through 44 Processing helix chain 'e' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY e 52 " --> pdb=" O PHE e 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER e 57 " --> pdb=" O ALA e 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET e 64 " --> pdb=" O THR e 61 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 19 removed outlier: 3.964A pdb=" N LYS f 16 " --> pdb=" O ALA f 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE f 19 " --> pdb=" O LYS f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 44 Processing helix chain 'f' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY f 52 " --> pdb=" O PHE f 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER f 57 " --> pdb=" O ALA f 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET f 64 " --> pdb=" O THR f 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS g 16 " --> pdb=" O ALA g 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE g 19 " --> pdb=" O LYS g 16 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 44 Processing helix chain 'g' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY g 52 " --> pdb=" O PHE g 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER g 57 " --> pdb=" O ALA g 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET g 64 " --> pdb=" O THR g 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS h 16 " --> pdb=" O ALA h 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE h 19 " --> pdb=" O LYS h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 24 through 44 Processing helix chain 'h' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY h 52 " --> pdb=" O PHE h 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER h 57 " --> pdb=" O ALA h 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET h 64 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS i 16 " --> pdb=" O ALA i 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE i 19 " --> pdb=" O LYS i 16 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 44 Processing helix chain 'i' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY i 52 " --> pdb=" O PHE i 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER i 57 " --> pdb=" O ALA i 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET i 64 " --> pdb=" O THR i 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS j 16 " --> pdb=" O ALA j 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE j 19 " --> pdb=" O LYS j 16 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 44 Processing helix chain 'j' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY j 52 " --> pdb=" O PHE j 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER j 57 " --> pdb=" O ALA j 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET j 64 " --> pdb=" O THR j 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS k 16 " --> pdb=" O ALA k 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE k 19 " --> pdb=" O LYS k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 44 Processing helix chain 'k' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY k 52 " --> pdb=" O PHE k 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER k 57 " --> pdb=" O ALA k 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET k 64 " --> pdb=" O THR k 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 9 through 19 removed outlier: 3.964A pdb=" N LYS l 16 " --> pdb=" O ALA l 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE l 19 " --> pdb=" O LYS l 16 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 44 Processing helix chain 'l' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY l 52 " --> pdb=" O PHE l 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER l 57 " --> pdb=" O ALA l 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET l 64 " --> pdb=" O THR l 61 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS m 16 " --> pdb=" O ALA m 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE m 19 " --> pdb=" O LYS m 16 " (cutoff:3.500A) Processing helix chain 'm' and resid 24 through 44 Processing helix chain 'm' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY m 52 " --> pdb=" O PHE m 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER m 57 " --> pdb=" O ALA m 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET m 64 " --> pdb=" O THR m 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS n 16 " --> pdb=" O ALA n 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE n 19 " --> pdb=" O LYS n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 44 Processing helix chain 'n' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY n 52 " --> pdb=" O PHE n 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER n 57 " --> pdb=" O ALA n 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET n 64 " --> pdb=" O THR n 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS o 16 " --> pdb=" O ALA o 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE o 19 " --> pdb=" O LYS o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 44 Processing helix chain 'o' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY o 52 " --> pdb=" O PHE o 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER o 57 " --> pdb=" O ALA o 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET o 64 " --> pdb=" O THR o 61 " (cutoff:3.500A) 1558 hydrogen bonds defined for protein. 2091 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: 7.03 Time building geometry restraints manager: 10.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3239 1.30 - 1.43: 5576 1.43 - 1.55: 12956 1.55 - 1.67: 205 1.67 - 1.80: 451 Bond restraints: 22427 Sorted by residual: bond pdb=" CB PHE Z 53 " pdb=" CG PHE Z 53 " ideal model delta sigma weight residual 1.502 1.419 0.083 2.30e-02 1.89e+03 1.29e+01 bond pdb=" CB PHE d 53 " pdb=" CG PHE d 53 " ideal model delta sigma weight residual 1.502 1.420 0.082 2.30e-02 1.89e+03 1.29e+01 bond pdb=" CB PHE H 53 " pdb=" CG PHE H 53 " ideal model delta sigma weight residual 1.502 1.420 0.082 2.30e-02 1.89e+03 1.28e+01 bond pdb=" CB PHE n 53 " pdb=" CG PHE n 53 " ideal model delta sigma weight residual 1.502 1.420 0.082 2.30e-02 1.89e+03 1.28e+01 bond pdb=" CD GLU b 33 " pdb=" OE1 GLU b 33 " ideal model delta sigma weight residual 1.249 1.181 0.068 1.90e-02 2.77e+03 1.28e+01 ... (remaining 22422 not shown) Histogram of bond angle deviations from ideal: 95.95 - 103.52: 410 103.52 - 111.10: 8666 111.10 - 118.67: 9493 118.67 - 126.24: 10951 126.24 - 133.82: 205 Bond angle restraints: 29725 Sorted by residual: angle pdb=" N MET l 43 " pdb=" CA MET l 43 " pdb=" C MET l 43 " ideal model delta sigma weight residual 111.07 116.58 -5.51 1.07e+00 8.73e-01 2.65e+01 angle pdb=" N MET E 43 " pdb=" CA MET E 43 " pdb=" C MET E 43 " ideal model delta sigma weight residual 111.07 116.55 -5.48 1.07e+00 8.73e-01 2.62e+01 angle pdb=" N MET P 43 " pdb=" CA MET P 43 " pdb=" C MET P 43 " ideal model delta sigma weight residual 111.07 116.54 -5.47 1.07e+00 8.73e-01 2.62e+01 angle pdb=" N MET C 43 " pdb=" CA MET C 43 " pdb=" C MET C 43 " ideal model delta sigma weight residual 111.07 116.54 -5.47 1.07e+00 8.73e-01 2.61e+01 angle pdb=" N MET O 43 " pdb=" CA MET O 43 " pdb=" C MET O 43 " ideal model delta sigma weight residual 111.07 116.54 -5.47 1.07e+00 8.73e-01 2.61e+01 ... (remaining 29720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.11: 11431 11.11 - 22.21: 1443 22.21 - 33.32: 205 33.32 - 44.42: 0 44.42 - 55.53: 123 Dihedral angle restraints: 13202 sinusoidal: 5699 harmonic: 7503 Sorted by residual: dihedral pdb=" C THR k 18 " pdb=" N THR k 18 " pdb=" CA THR k 18 " pdb=" CB THR k 18 " ideal model delta harmonic sigma weight residual -122.00 -129.55 7.55 0 2.50e+00 1.60e-01 9.12e+00 dihedral pdb=" C THR V 18 " pdb=" N THR V 18 " pdb=" CA THR V 18 " pdb=" CB THR V 18 " ideal model delta harmonic sigma weight residual -122.00 -129.55 7.55 0 2.50e+00 1.60e-01 9.11e+00 dihedral pdb=" C THR i 18 " pdb=" N THR i 18 " pdb=" CA THR i 18 " pdb=" CB THR i 18 " ideal model delta harmonic sigma weight residual -122.00 -129.54 7.54 0 2.50e+00 1.60e-01 9.09e+00 ... (remaining 13199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1932 0.077 - 0.154: 1099 0.154 - 0.231: 254 0.231 - 0.308: 77 0.308 - 0.385: 41 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CA THR V 18 " pdb=" N THR V 18 " pdb=" C THR V 18 " pdb=" CB THR V 18 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA THR k 18 " pdb=" N THR k 18 " pdb=" C THR k 18 " pdb=" CB THR k 18 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA THR B 18 " pdb=" N THR B 18 " pdb=" C THR B 18 " pdb=" CB THR B 18 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 3400 not shown) Planarity restraints: 3239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR k 69 " -0.040 2.00e-02 2.50e+03 8.16e-02 6.66e+01 pdb=" C TYR k 69 " 0.141 2.00e-02 2.50e+03 pdb=" O TYR k 69 " -0.051 2.00e-02 2.50e+03 pdb=" OXT TYR k 69 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR e 69 " 0.040 2.00e-02 2.50e+03 8.15e-02 6.65e+01 pdb=" C TYR e 69 " -0.141 2.00e-02 2.50e+03 pdb=" O TYR e 69 " 0.051 2.00e-02 2.50e+03 pdb=" OXT TYR e 69 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR Y 69 " -0.040 2.00e-02 2.50e+03 8.15e-02 6.64e+01 pdb=" C TYR Y 69 " 0.141 2.00e-02 2.50e+03 pdb=" O TYR Y 69 " -0.051 2.00e-02 2.50e+03 pdb=" OXT TYR Y 69 " -0.050 2.00e-02 2.50e+03 ... (remaining 3236 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9241 2.86 - 3.37: 23422 3.37 - 3.88: 36991 3.88 - 4.39: 46718 4.39 - 4.90: 72099 Nonbonded interactions: 188471 Sorted by model distance: nonbonded pdb=" O2 LHG O 101 " pdb=" O3 LHG O 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG K 101 " pdb=" O3 LHG K 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG V 101 " pdb=" O3 LHG V 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG U 101 " pdb=" O3 LHG U 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG o 101 " pdb=" O3 LHG o 101 " model vdw 2.348 2.432 ... (remaining 188466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 22140 22140 False True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 41 5.49 5 S 205 5.16 5 C 14801 2.51 5 N 3075 2.21 5 O 4018 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 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: 1.030 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.100 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.110 Process input model: 61.500 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.450 Internal consistency checks: 0.000 Total: 71.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.019 0.083 22427 Angle : 1.513 5.865 29725 Chirality : 0.104 0.385 3403 Planarity : 0.012 0.082 3239 Dihedral : 10.554 55.527 8446 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % 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: 1.16 (0.15), residues: 2624 helix: 0.28 (0.09), residues: 2091 sheet: None (None), residues: 0 loop : 3.70 (0.28), residues: 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 999 time to evaluate : 2.294 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 999 average time/residue: 0.3438 time to fit residues: 347.4078 Evaluate side-chains 684 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 684 time to evaluate : 2.352 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN m 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.047 22427 Angle : 0.485 5.353 29725 Chirality : 0.036 0.132 3403 Planarity : 0.005 0.020 3239 Dihedral : 12.251 80.975 4223 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer Outliers : 0.05 % 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: 1.47 (0.15), residues: 2624 helix: 0.36 (0.10), residues: 1804 sheet: None (None), residues: 0 loop : 3.03 (0.24), residues: 820 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 825 time to evaluate : 2.586 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 825 average time/residue: 0.3167 time to fit residues: 265.5416 Evaluate side-chains 636 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 636 time to evaluate : 2.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 241 optimal weight: 0.0670 chunk 199 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 76 optimal weight: 0.0470 chunk 179 optimal weight: 2.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.043 22427 Angle : 0.459 7.742 29725 Chirality : 0.035 0.113 3403 Planarity : 0.004 0.017 3239 Dihedral : 12.202 88.730 4223 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer Outliers : 0.00 % 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: 0.99 (0.15), residues: 2624 helix: 0.26 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : 2.13 (0.21), residues: 820 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 750 time to evaluate : 2.533 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 750 average time/residue: 0.3399 time to fit residues: 259.6669 Evaluate side-chains 602 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 602 time to evaluate : 2.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.044 22427 Angle : 0.521 8.321 29725 Chirality : 0.036 0.128 3403 Planarity : 0.004 0.017 3239 Dihedral : 13.842 78.853 4223 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer Outliers : 0.05 % 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: 0.17 (0.15), residues: 2624 helix: -0.09 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : 1.08 (0.19), residues: 820 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 731 time to evaluate : 2.536 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 732 average time/residue: 0.3238 time to fit residues: 240.7585 Evaluate side-chains 590 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 590 time to evaluate : 2.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 30.0000 chunk 134 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN J 22 GLN ** m 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.043 22427 Angle : 0.495 6.938 29725 Chirality : 0.035 0.135 3403 Planarity : 0.004 0.016 3239 Dihedral : 13.340 59.688 4223 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer Outliers : 0.00 % 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: 0.17 (0.15), residues: 2624 helix: 0.02 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : 0.78 (0.19), residues: 820 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 701 time to evaluate : 2.689 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 701 average time/residue: 0.3309 time to fit residues: 235.9334 Evaluate side-chains 572 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 572 time to evaluate : 2.495 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.0980 chunk 214 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 197 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 78 optimal weight: 9.9990 chunk 124 optimal weight: 0.0970 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN J 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.040 22427 Angle : 0.479 8.752 29725 Chirality : 0.034 0.120 3403 Planarity : 0.004 0.017 3239 Dihedral : 12.510 59.770 4223 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer Outliers : 0.00 % 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: -0.18 (0.15), residues: 2624 helix: 0.10 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : -0.29 (0.19), residues: 820 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 711 time to evaluate : 2.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 711 average time/residue: 0.3232 time to fit residues: 233.9637 Evaluate side-chains 575 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 575 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN J 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.041 22427 Angle : 0.488 7.636 29725 Chirality : 0.035 0.132 3403 Planarity : 0.004 0.017 3239 Dihedral : 12.502 59.346 4223 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer Outliers : 0.00 % 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: 0.46 (0.15), residues: 2624 helix: 0.19 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : 1.03 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 700 time to evaluate : 2.713 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 700 average time/residue: 0.3367 time to fit residues: 239.8302 Evaluate side-chains 578 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 578 time to evaluate : 2.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 150 optimal weight: 30.0000 chunk 161 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 186 optimal weight: 30.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 22 GLN I 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.7369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.039 22427 Angle : 0.499 8.702 29725 Chirality : 0.034 0.123 3403 Planarity : 0.004 0.016 3239 Dihedral : 12.263 59.745 4223 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer Outliers : 0.00 % 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: 0.53 (0.15), residues: 2624 helix: 0.19 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : 1.18 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 685 time to evaluate : 2.311 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 685 average time/residue: 0.3322 time to fit residues: 231.4507 Evaluate side-chains 573 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 573 time to evaluate : 2.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN J 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.6993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.041 22427 Angle : 0.568 9.112 29725 Chirality : 0.036 0.147 3403 Planarity : 0.004 0.018 3239 Dihedral : 13.597 59.944 4223 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer Outliers : 0.00 % 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: -0.13 (0.15), residues: 2624 helix: -0.04 (0.11), residues: 1845 sheet: None (None), residues: 0 loop : 0.21 (0.19), residues: 779 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 672 time to evaluate : 2.297 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.3328 time to fit residues: 227.5951 Evaluate side-chains 546 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 546 time to evaluate : 2.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 162 optimal weight: 30.0000 chunk 245 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 150 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 chunk 155 optimal weight: 0.0770 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.7439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.039 22427 Angle : 0.530 9.101 29725 Chirality : 0.034 0.144 3403 Planarity : 0.004 0.017 3239 Dihedral : 12.579 59.986 4223 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer Outliers : 0.00 % 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: 0.03 (0.15), residues: 2624 helix: 0.03 (0.11), residues: 1845 sheet: None (None), residues: 0 loop : 0.42 (0.19), residues: 779 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield and 0 Emsley and 2624 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 687 time to evaluate : 2.339 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 687 average time/residue: 0.3228 time to fit residues: 225.7691 Evaluate side-chains 558 residues out of total 2132 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 558 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 54 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN J 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154495 restraints weight = 31178.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157386 restraints weight = 14947.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.159052 restraints weight = 8236.630| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.003 0.040 22427 ANGLE : 0.541 9.222 29725 CHIRALITY : 0.034 0.147 3403 PLANARITY : 0.004 0.018 3239 DIHEDRAL : 12.318 59.852 4223 MIN NONBONDED DISTANCE : 2.155 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 9.22 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 0.42 % FAVORED : 99.58 % ROTAMER OUTLIERS : 0.00 % 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: 0.15 (0.15), RESIDUES: 2624 HELIX: 0.10 (0.11), RESIDUES: 1845 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 0.52 (0.20), RESIDUES: 779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.7601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.040 22427 Angle : 0.541 9.222 29725 Chirality : 0.034 0.147 3403 Planarity : 0.004 0.018 3239 Dihedral : 12.318 59.852 4223 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer Outliers : 0.00 % 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: 0.15 (0.15), residues: 2624 helix: 0.10 (0.11), residues: 1845 sheet: None (None), residues: 0 loop : 0.52 (0.20), residues: 779 =============================================================================== Job complete usr+sys time: 4627.41 seconds wall clock time: 85 minutes 46.00 seconds (5146.00 seconds total)