Starting phenix.real_space_refine (version: dev) on Thu Dec 22 00:32:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/12_2022/6utf_20877.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/12_2022/6utf_20877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/12_2022/6utf_20877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/12_2022/6utf_20877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/12_2022/6utf_20877.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/12_2022/6utf_20877.pdb" } resolution = 3.4 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= 0.062 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "O ARG 10": "NH1" <-> "NH2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "Q ARG 10": "NH1" <-> "NH2" Residue "R ARG 10": "NH1" <-> "NH2" Residue "S ARG 10": "NH1" <-> "NH2" Residue "T ARG 10": "NH1" <-> "NH2" Residue "U ARG 10": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 46494 Number of models: 1 Model: "" Number of chains: 28 Chain: "Z" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "M" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "1" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "N" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "H" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "V" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "I" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "W" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "J" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "X" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "K" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "Y" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "A" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "D" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "G" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "O" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "P" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "Q" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "R" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "S" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "T" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "U" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ARG A 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG A 28 " occ=0.50 residue: pdb=" N VAL A 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL A 77 " occ=0.50 residue: pdb=" N ARG B 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 28 " occ=0.50 residue: pdb=" N VAL B 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL B 77 " occ=0.50 residue: pdb=" N ARG C 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 28 " occ=0.50 residue: pdb=" N VAL C 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL C 77 " occ=0.50 residue: pdb=" N ARG D 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG D 28 " occ=0.50 residue: pdb=" N VAL D 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D 77 " occ=0.50 residue: pdb=" N ARG E 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG E 28 " occ=0.50 residue: pdb=" N VAL E 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL E 77 " occ=0.50 residue: pdb=" N ARG F 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG F 28 " occ=0.50 residue: pdb=" N ARG G 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG G 28 " occ=0.50 Time building chain proxies: 24.96, per 1000 atoms: 0.54 Number of scatterers: 46494 At special positions: 0 Unit cell: (132.98, 132.98, 173.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 8981 8.00 N 7847 7.00 C 29470 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 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: 17.14 Conformation dependent library (CDL) restraints added in 6.5 seconds 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11074 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 56 sheets defined 41.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 removed outlier: 4.037A pdb=" N VAL Z 134 " --> pdb=" O GLY Z 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 165 Processing helix chain 'Z' and resid 188 through 200 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL M 134 " --> pdb=" O GLY M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 165 Processing helix chain 'M' and resid 188 through 200 Processing helix chain '1' and resid 48 through 71 Processing helix chain '1' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL 1 90 " --> pdb=" O MET 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL 1 134 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 165 Processing helix chain '1' and resid 188 through 200 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 3.919A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL N 134 " --> pdb=" O GLY N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 165 Processing helix chain 'N' and resid 188 through 200 Processing helix chain '2' and resid 48 through 71 Processing helix chain '2' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL 2 90 " --> pdb=" O MET 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL 2 134 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 165 Processing helix chain '2' and resid 188 through 200 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.917A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 165 Processing helix chain 'H' and resid 188 through 200 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 165 Processing helix chain 'V' and resid 188 through 200 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 4.035A pdb=" N VAL I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 165 Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL W 134 " --> pdb=" O GLY W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 165 Processing helix chain 'W' and resid 188 through 200 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 removed outlier: 4.037A pdb=" N VAL J 134 " --> pdb=" O GLY J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 165 Processing helix chain 'J' and resid 188 through 200 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 3.917A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 removed outlier: 4.035A pdb=" N VAL X 134 " --> pdb=" O GLY X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 165 Processing helix chain 'X' and resid 188 through 200 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 removed outlier: 4.037A pdb=" N VAL K 134 " --> pdb=" O GLY K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 165 Processing helix chain 'K' and resid 188 through 200 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 removed outlier: 4.037A pdb=" N VAL Y 134 " --> pdb=" O GLY Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 165 Processing helix chain 'Y' and resid 188 through 200 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.917A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 165 Processing helix chain 'L' and resid 188 through 200 Processing helix chain 'A' and resid 21 through 33 removed outlier: 3.660A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.613A pdb=" N ILE A 64 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 123 removed outlier: 4.072A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.568A pdb=" N ARG A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 225 through 231 removed outlier: 3.533A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.622A pdb=" N ILE B 64 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 123 removed outlier: 4.049A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.522A pdb=" N ARG B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 Processing helix chain 'B' and resid 225 through 231 removed outlier: 3.543A pdb=" N LYS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.612A pdb=" N ILE C 64 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 123 removed outlier: 4.069A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.534A pdb=" N ARG C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 225 through 231 removed outlier: 3.534A pdb=" N LYS C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 32 Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.625A pdb=" N ILE D 64 " --> pdb=" O GLN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 123 removed outlier: 4.060A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 removed outlier: 3.543A pdb=" N ARG D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 199 Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.512A pdb=" N LYS D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.664A pdb=" N ILE E 64 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU E 65 " --> pdb=" O ASN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 103 Processing helix chain 'E' and resid 108 through 123 removed outlier: 4.097A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 removed outlier: 3.524A pdb=" N ARG E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 199 Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.554A pdb=" N LYS E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 32 Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.626A pdb=" N ILE F 64 " --> pdb=" O GLN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 123 removed outlier: 4.034A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 removed outlier: 3.531A pdb=" N ARG F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 Processing helix chain 'F' and resid 225 through 231 removed outlier: 3.507A pdb=" N LYS F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 Processing helix chain 'G' and resid 60 through 65 removed outlier: 3.650A pdb=" N ILE G 64 " --> pdb=" O GLN G 61 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU G 65 " --> pdb=" O ASN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 4.058A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 removed outlier: 3.541A pdb=" N ARG G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 199 Processing helix chain 'G' and resid 225 through 231 removed outlier: 3.571A pdb=" N LYS G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 28 Processing helix chain 'O' and resid 30 through 34 removed outlier: 3.525A pdb=" N GLY O 34 " --> pdb=" O VAL O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 103 Processing helix chain 'O' and resid 108 through 126 removed outlier: 4.097A pdb=" N LEU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 180 removed outlier: 3.658A pdb=" N TYR O 180 " --> pdb=" O LEU O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 201 Processing helix chain 'O' and resid 225 through 233 removed outlier: 3.710A pdb=" N VAL O 229 " --> pdb=" O ASP O 225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS O 230 " --> pdb=" O GLN O 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS O 231 " --> pdb=" O GLU O 227 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE O 232 " --> pdb=" O GLU O 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 32 Processing helix chain 'P' and resid 81 through 103 Processing helix chain 'P' and resid 108 through 126 removed outlier: 4.176A pdb=" N LEU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 180 removed outlier: 3.656A pdb=" N TYR P 180 " --> pdb=" O LEU P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 201 Processing helix chain 'P' and resid 225 through 233 removed outlier: 3.709A pdb=" N VAL P 229 " --> pdb=" O ASP P 225 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS P 230 " --> pdb=" O GLN P 226 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS P 231 " --> pdb=" O GLU P 227 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE P 232 " --> pdb=" O GLU P 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 28 Processing helix chain 'Q' and resid 30 through 34 removed outlier: 3.507A pdb=" N GLY Q 34 " --> pdb=" O VAL Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 103 Processing helix chain 'Q' and resid 108 through 126 removed outlier: 4.171A pdb=" N LEU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 180 removed outlier: 3.621A pdb=" N TYR Q 180 " --> pdb=" O LEU Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 201 Processing helix chain 'Q' and resid 225 through 233 removed outlier: 3.709A pdb=" N VAL Q 229 " --> pdb=" O ASP Q 225 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS Q 230 " --> pdb=" O GLN Q 226 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE Q 232 " --> pdb=" O GLU Q 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 32 Processing helix chain 'R' and resid 81 through 103 Processing helix chain 'R' and resid 108 through 126 removed outlier: 4.069A pdb=" N LEU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 180 removed outlier: 3.649A pdb=" N TYR R 180 " --> pdb=" O LEU R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 201 Processing helix chain 'R' and resid 225 through 233 removed outlier: 3.717A pdb=" N VAL R 229 " --> pdb=" O ASP R 225 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS R 231 " --> pdb=" O GLU R 227 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE R 232 " --> pdb=" O GLU R 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 28 Processing helix chain 'S' and resid 30 through 34 Processing helix chain 'S' and resid 81 through 103 Processing helix chain 'S' and resid 108 through 126 removed outlier: 4.145A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 180 removed outlier: 3.673A pdb=" N TYR S 180 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 201 Processing helix chain 'S' and resid 225 through 233 removed outlier: 3.701A pdb=" N VAL S 229 " --> pdb=" O ASP S 225 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS S 230 " --> pdb=" O GLN S 226 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS S 231 " --> pdb=" O GLU S 227 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE S 232 " --> pdb=" O GLU S 228 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 28 Processing helix chain 'T' and resid 30 through 34 Processing helix chain 'T' and resid 81 through 103 Processing helix chain 'T' and resid 108 through 126 removed outlier: 4.161A pdb=" N LEU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 180 removed outlier: 3.653A pdb=" N TYR T 180 " --> pdb=" O LEU T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 201 Processing helix chain 'T' and resid 225 through 233 removed outlier: 3.706A pdb=" N VAL T 229 " --> pdb=" O ASP T 225 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS T 230 " --> pdb=" O GLN T 226 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS T 231 " --> pdb=" O GLU T 227 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE T 232 " --> pdb=" O GLU T 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 28 Processing helix chain 'U' and resid 30 through 34 removed outlier: 3.513A pdb=" N GLY U 34 " --> pdb=" O VAL U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 103 Processing helix chain 'U' and resid 108 through 126 removed outlier: 4.175A pdb=" N LEU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 180 removed outlier: 3.657A pdb=" N TYR U 180 " --> pdb=" O LEU U 176 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 Processing helix chain 'U' and resid 225 through 233 removed outlier: 3.704A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS U 230 " --> pdb=" O GLN U 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS U 231 " --> pdb=" O GLU U 227 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE U 232 " --> pdb=" O GLU U 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR Z 179 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL Z 110 " --> pdb=" O ASP Z 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP Z 122 " --> pdb=" O VAL Z 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Z 112 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 124 through 125 removed outlier: 3.612A pdb=" N THR M 179 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.610A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU M 100 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL M 110 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP M 122 " --> pdb=" O VAL M 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER M 112 " --> pdb=" O VAL M 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 124 through 125 removed outlier: 3.612A pdb=" N THR 1 179 " --> pdb=" O GLY 1 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR 1 41 " --> pdb=" O ILE 1 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU 1 100 " --> pdb=" O THR 1 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL 1 110 " --> pdb=" O ASP 1 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP 1 122 " --> pdb=" O VAL 1 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 1 112 " --> pdb=" O VAL 1 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR N 179 " --> pdb=" O GLY N 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.610A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU N 100 " --> pdb=" O THR N 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL N 110 " --> pdb=" O ASP N 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP N 122 " --> pdb=" O VAL N 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER N 112 " --> pdb=" O VAL N 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR 2 179 " --> pdb=" O GLY 2 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '2' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR 2 41 " --> pdb=" O ILE 2 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU 2 100 " --> pdb=" O THR 2 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL 2 110 " --> pdb=" O ASP 2 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP 2 122 " --> pdb=" O VAL 2 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER 2 112 " --> pdb=" O VAL 2 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR H 179 " --> pdb=" O GLY H 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.610A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU H 100 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL H 110 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP H 122 " --> pdb=" O VAL H 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER H 112 " --> pdb=" O VAL H 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR V 179 " --> pdb=" O GLY V 183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU V 100 " --> pdb=" O THR V 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL V 110 " --> pdb=" O ASP V 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP V 122 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER V 112 " --> pdb=" O VAL V 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 124 through 125 removed outlier: 3.612A pdb=" N THR I 179 " --> pdb=" O GLY I 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU I 100 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL I 110 " --> pdb=" O ASP I 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP I 122 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER I 112 " --> pdb=" O VAL I 120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR W 179 " --> pdb=" O GLY W 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU W 100 " --> pdb=" O THR W 44 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL W 110 " --> pdb=" O ASP W 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP W 122 " --> pdb=" O VAL W 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER W 112 " --> pdb=" O VAL W 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 124 through 125 removed outlier: 3.612A pdb=" N THR J 179 " --> pdb=" O GLY J 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU J 100 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL J 110 " --> pdb=" O ASP J 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP J 122 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER J 112 " --> pdb=" O VAL J 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR X 179 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU X 100 " --> pdb=" O THR X 44 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL X 110 " --> pdb=" O ASP X 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP X 122 " --> pdb=" O VAL X 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER X 112 " --> pdb=" O VAL X 120 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 124 through 125 removed outlier: 3.612A pdb=" N THR K 179 " --> pdb=" O GLY K 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU K 100 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL K 110 " --> pdb=" O ASP K 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP K 122 " --> pdb=" O VAL K 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER K 112 " --> pdb=" O VAL K 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR Y 179 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.610A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU Y 100 " --> pdb=" O THR Y 44 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL Y 110 " --> pdb=" O ASP Y 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP Y 122 " --> pdb=" O VAL Y 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Y 112 " --> pdb=" O VAL Y 120 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR L 179 " --> pdb=" O GLY L 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL L 110 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP L 122 " --> pdb=" O VAL L 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER L 112 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 162 through 165 removed outlier: 3.589A pdb=" N GLY A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE A 212 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AD4, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.577A pdb=" N GLY B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE B 212 " --> pdb=" O TYR B 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AD6, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.565A pdb=" N GLY C 45 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AD8, first strand: chain 'D' and resid 162 through 165 removed outlier: 3.597A pdb=" N GLY D 45 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE D 212 " --> pdb=" O TYR D 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 67 through 69 Processing sheet with id=AE1, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.571A pdb=" N GLY E 45 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE E 212 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AE3, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.610A pdb=" N GLY F 45 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AE5, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.565A pdb=" N GLY G 45 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.505A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 162 through 165 removed outlier: 3.538A pdb=" N GLY O 45 " --> pdb=" O PHE O 42 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER O 214 " --> pdb=" O ARG O 222 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 68 through 69 Processing sheet with id=AE9, first strand: chain 'P' and resid 162 through 165 removed outlier: 3.528A pdb=" N GLY P 45 " --> pdb=" O PHE P 42 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER P 214 " --> pdb=" O ARG P 222 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 68 through 69 Processing sheet with id=AF2, first strand: chain 'Q' and resid 162 through 165 removed outlier: 3.537A pdb=" N GLY Q 45 " --> pdb=" O PHE Q 42 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER Q 214 " --> pdb=" O ARG Q 222 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 68 through 69 Processing sheet with id=AF4, first strand: chain 'R' and resid 162 through 165 removed outlier: 3.531A pdb=" N GLY R 45 " --> pdb=" O PHE R 42 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER R 214 " --> pdb=" O ARG R 222 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 68 through 69 Processing sheet with id=AF6, first strand: chain 'S' and resid 162 through 165 removed outlier: 3.530A pdb=" N GLY S 45 " --> pdb=" O PHE S 42 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER S 214 " --> pdb=" O ARG S 222 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 68 through 69 Processing sheet with id=AF8, first strand: chain 'T' and resid 162 through 165 removed outlier: 3.519A pdb=" N GLY T 45 " --> pdb=" O PHE T 42 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER T 214 " --> pdb=" O ARG T 222 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 68 through 69 Processing sheet with id=AG1, first strand: chain 'U' and resid 162 through 165 removed outlier: 3.517A pdb=" N GLY U 45 " --> pdb=" O PHE U 42 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER U 214 " --> pdb=" O ARG U 222 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 68 through 69 2552 hydrogen bonds defined for protein. 7341 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: 17.72 Time building geometry restraints manager: 18.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8035 1.31 - 1.43: 11154 1.43 - 1.56: 27505 1.56 - 1.68: 24 1.68 - 1.80: 378 Bond restraints: 47096 Sorted by residual: bond pdb=" CA LEU D 21 " pdb=" CB LEU D 21 " ideal model delta sigma weight residual 1.525 1.453 0.072 1.47e-02 4.63e+03 2.40e+01 bond pdb=" CB MET G 40 " pdb=" CG MET G 40 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.38e+01 bond pdb=" CB MET E 40 " pdb=" CG MET E 40 " ideal model delta sigma weight residual 1.520 1.416 0.104 3.00e-02 1.11e+03 1.21e+01 bond pdb=" CB MET A 40 " pdb=" CG MET A 40 " ideal model delta sigma weight residual 1.520 1.418 0.102 3.00e-02 1.11e+03 1.17e+01 bond pdb=" CB MET B 40 " pdb=" CG MET B 40 " ideal model delta sigma weight residual 1.520 1.418 0.102 3.00e-02 1.11e+03 1.15e+01 ... (remaining 47091 not shown) Histogram of bond angle deviations from ideal: 95.09 - 104.08: 551 104.08 - 113.07: 25393 113.07 - 122.05: 28954 122.05 - 131.04: 8628 131.04 - 140.03: 62 Bond angle restraints: 63588 Sorted by residual: angle pdb=" C LEU P 207 " pdb=" N LYS P 208 " pdb=" CA LYS P 208 " ideal model delta sigma weight residual 121.54 134.42 -12.88 1.91e+00 2.74e-01 4.54e+01 angle pdb=" C LEU O 207 " pdb=" N LYS O 208 " pdb=" CA LYS O 208 " ideal model delta sigma weight residual 121.54 134.39 -12.85 1.91e+00 2.74e-01 4.53e+01 angle pdb=" C LEU S 207 " pdb=" N LYS S 208 " pdb=" CA LYS S 208 " ideal model delta sigma weight residual 121.54 134.38 -12.84 1.91e+00 2.74e-01 4.52e+01 angle pdb=" C LEU U 207 " pdb=" N LYS U 208 " pdb=" CA LYS U 208 " ideal model delta sigma weight residual 121.54 134.37 -12.83 1.91e+00 2.74e-01 4.51e+01 angle pdb=" C LEU R 207 " pdb=" N LYS R 208 " pdb=" CA LYS R 208 " ideal model delta sigma weight residual 121.54 134.34 -12.80 1.91e+00 2.74e-01 4.49e+01 ... (remaining 63583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 27195 15.40 - 30.79: 1249 30.79 - 46.19: 300 46.19 - 61.58: 19 61.58 - 76.98: 49 Dihedral angle restraints: 28812 sinusoidal: 11473 harmonic: 17339 Sorted by residual: dihedral pdb=" CA ASP R 9 " pdb=" C ASP R 9 " pdb=" N ARG R 10 " pdb=" CA ARG R 10 " ideal model delta harmonic sigma weight residual 180.00 118.64 61.36 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA ASN K 24 " pdb=" C ASN K 24 " pdb=" N PHE K 25 " pdb=" CA PHE K 25 " ideal model delta harmonic sigma weight residual 180.00 120.64 59.36 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA ASN 1 24 " pdb=" C ASN 1 24 " pdb=" N PHE 1 25 " pdb=" CA PHE 1 25 " ideal model delta harmonic sigma weight residual 180.00 120.66 59.34 0 5.00e+00 4.00e-02 1.41e+02 ... (remaining 28809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 5878 0.070 - 0.140: 1204 0.140 - 0.211: 279 0.211 - 0.281: 55 0.281 - 0.351: 32 Chirality restraints: 7448 Sorted by residual: chirality pdb=" CB VAL C 74 " pdb=" CA VAL C 74 " pdb=" CG1 VAL C 74 " pdb=" CG2 VAL C 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB VAL B 74 " pdb=" CA VAL B 74 " pdb=" CG1 VAL B 74 " pdb=" CG2 VAL B 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB VAL G 74 " pdb=" CA VAL G 74 " pdb=" CG1 VAL G 74 " pdb=" CG2 VAL G 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 7445 not shown) Planarity restraints: 8162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP Q 9 " -0.029 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C ASP Q 9 " 0.099 2.00e-02 2.50e+03 pdb=" O ASP Q 9 " -0.036 2.00e-02 2.50e+03 pdb=" N ARG Q 10 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 10 " -0.098 9.50e-02 1.11e+02 6.15e-02 2.43e+01 pdb=" NE ARG Q 10 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG Q 10 " 0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 10 " -0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 10 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR Q 26 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C TYR Q 26 " -0.068 2.00e-02 2.50e+03 pdb=" O TYR Q 26 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA Q 27 " 0.023 2.00e-02 2.50e+03 ... (remaining 8159 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 530 2.61 - 3.18: 38473 3.18 - 3.75: 73362 3.75 - 4.33: 100779 4.33 - 4.90: 167504 Nonbonded interactions: 380648 Sorted by model distance: nonbonded pdb=" O GLU S 25 " pdb=" O LEU S 28 " model vdw 2.036 3.040 nonbonded pdb=" O GLU U 25 " pdb=" O LEU U 28 " model vdw 2.042 3.040 nonbonded pdb=" O GLU O 25 " pdb=" O LEU O 28 " model vdw 2.044 3.040 nonbonded pdb=" O GLU Q 25 " pdb=" O LEU Q 28 " model vdw 2.048 3.040 nonbonded pdb=" O GLU T 25 " pdb=" O LEU T 28 " model vdw 2.062 3.040 ... (remaining 380643 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 '1' selection = chain '2' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = (chain 'A' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'B' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'C' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'D' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'E' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'F' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'G' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'O' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'P' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'Q' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'R' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'S' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'T' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'U' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 29470 2.51 5 N 7847 2.21 5 O 8981 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=0.50 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: 1.690 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: 0.060 Extract box with map and model: 11.430 Check model and map are aligned: 0.650 Convert atoms to be neutral: 0.380 Process input model: 109.230 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.009 0.117 47096 Z= 0.567 Angle : 1.283 17.030 63588 Z= 0.718 Chirality : 0.066 0.351 7448 Planarity : 0.007 0.068 8162 Dihedral : 10.410 76.979 17738 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.69 % Favored : 93.86 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.27 (0.09), residues: 5957 helix: -1.76 (0.08), residues: 2289 sheet: -1.45 (0.14), residues: 1211 loop : -2.85 (0.10), residues: 2457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2600 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 2565 time to evaluate : 5.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 35 outliers final: 11 residues processed: 2586 average time/residue: 0.6312 time to fit residues: 2567.2619 Evaluate side-chains 1248 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1237 time to evaluate : 5.371 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3743 time to fit residues: 15.2924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 0.9990 chunk 445 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 460 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 280 optimal weight: 0.0470 chunk 343 optimal weight: 7.9990 chunk 533 optimal weight: 2.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 85 ASN Z 191 GLN M 85 ASN M 89 GLN 1 30 ASN 1 85 ASN ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 GLN N 191 GLN 2 30 ASN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 191 GLN I 191 GLN W 88 ASN W 191 GLN J 89 GLN J 191 GLN K 191 GLN Y 85 ASN Y 191 GLN L 141 GLN C 68 GLN C 98 GLN C 183 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN F 68 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 GLN P 23 GLN P 122 GLN P 143 GLN Q 23 GLN Q 143 GLN R 23 GLN S 23 GLN S 143 GLN T 23 GLN T 143 GLN T 226 GLN U 23 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 47096 Z= 0.249 Angle : 0.843 22.160 63588 Z= 0.416 Chirality : 0.047 0.243 7448 Planarity : 0.005 0.111 8162 Dihedral : 6.523 53.793 6608 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.73 % Favored : 95.15 % Rotamer Outliers : 4.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.82 (0.10), residues: 5957 helix: 0.31 (0.10), residues: 2303 sheet: -1.43 (0.13), residues: 1288 loop : -2.61 (0.11), residues: 2366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1690 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1455 time to evaluate : 5.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 235 outliers final: 113 residues processed: 1607 average time/residue: 0.5558 time to fit residues: 1479.7745 Evaluate side-chains 1292 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1179 time to evaluate : 5.322 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 0 residues processed: 113 average time/residue: 0.3882 time to fit residues: 91.1059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.2714 > 50: distance: 32 - 41: 24.774 distance: 41 - 42: 4.554 distance: 42 - 43: 19.057 distance: 42 - 45: 9.017 distance: 43 - 44: 18.061 distance: 43 - 48: 14.181 distance: 45 - 46: 21.356 distance: 45 - 47: 20.301 distance: 48 - 49: 29.563 distance: 49 - 50: 34.084 distance: 49 - 52: 12.090 distance: 50 - 51: 43.932 distance: 50 - 55: 11.881 distance: 52 - 53: 27.090 distance: 52 - 54: 40.625 distance: 55 - 56: 14.535 distance: 56 - 57: 14.434 distance: 56 - 59: 33.502 distance: 57 - 58: 28.501 distance: 57 - 63: 33.924 distance: 59 - 60: 41.210 distance: 60 - 61: 11.269 distance: 61 - 62: 26.511 distance: 63 - 64: 37.427 distance: 64 - 65: 19.141 distance: 64 - 67: 5.884 distance: 65 - 66: 14.556 distance: 65 - 72: 16.019 distance: 69 - 70: 3.622 distance: 72 - 73: 5.313 distance: 73 - 74: 35.898 distance: 73 - 76: 19.171 distance: 74 - 75: 35.926 distance: 74 - 80: 14.890 distance: 76 - 77: 5.333 distance: 77 - 78: 10.973 distance: 77 - 79: 11.767 distance: 80 - 81: 14.400 distance: 81 - 82: 18.464 distance: 81 - 84: 10.674 distance: 82 - 83: 6.368 distance: 82 - 91: 36.391 distance: 84 - 85: 18.102 distance: 85 - 86: 13.538 distance: 85 - 87: 19.436 distance: 86 - 88: 18.058 distance: 87 - 89: 13.177 distance: 88 - 90: 9.638 distance: 89 - 90: 9.493 distance: 91 - 92: 5.905 distance: 92 - 93: 18.218 distance: 92 - 95: 11.105 distance: 93 - 94: 17.885 distance: 93 - 99: 22.950 distance: 95 - 96: 23.929 distance: 95 - 97: 29.012 distance: 96 - 98: 9.633 distance: 99 - 100: 8.055 distance: 100 - 101: 14.037 distance: 100 - 103: 27.553 distance: 101 - 102: 4.348 distance: 101 - 107: 3.774 distance: 103 - 104: 13.387 distance: 104 - 105: 20.955 distance: 105 - 106: 27.778 distance: 107 - 108: 6.538 distance: 108 - 109: 30.338 distance: 108 - 111: 38.437 distance: 109 - 110: 29.912 distance: 109 - 117: 4.283 distance: 111 - 112: 40.602 distance: 112 - 113: 15.282 distance: 113 - 115: 5.642 distance: 114 - 116: 5.282 distance: 115 - 116: 11.499 distance: 117 - 118: 39.985 distance: 118 - 119: 34.261 distance: 118 - 121: 46.885 distance: 119 - 120: 7.308 distance: 119 - 126: 31.345 distance: 121 - 122: 42.337 distance: 122 - 123: 41.954 distance: 123 - 124: 42.365 distance: 124 - 125: 9.528