Starting phenix.real_space_refine (version: dev) on Wed May 18 01:20:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/05_2022/6utf_20877.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/05_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_20877/05_2022/6utf_20877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/05_2022/6utf_20877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/05_2022/6utf_20877.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/05_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 None Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 25.12, 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: 18.68 Conformation dependent library (CDL) restraints added in 6.8 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: 2.49 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: 18.11 Time building geometry restraints manager: 20.08 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 11.360 Check model and map are aligned: 0.650 Convert atoms to be neutral: 0.410 Process input model: 114.310 Find NCS groups from input model: 3.630 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.930 ------------------------------------------------------------------------------- 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 : 5.830 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: 0.6672 time to fit residues: 2725.6062 Evaluate side-chains 1247 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1236 time to evaluate : 5.656 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3989 time to fit residues: 16.0016 ------------------------------------------------------------------------------- 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: 1.9990 chunk 343 optimal weight: 7.9990 chunk 533 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 A 62 ASN A 97 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 47096 Z= 0.259 Angle : 0.840 22.107 63588 Z= 0.415 Chirality : 0.047 0.250 7448 Planarity : 0.005 0.114 8162 Dihedral : 6.485 53.571 6608 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.80 % Favored : 95.08 % Rotamer Outliers : 5.37 % 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: -1.81 (0.10), residues: 5957 helix: 0.33 (0.10), residues: 2303 sheet: -1.42 (0.13), residues: 1288 loop : -2.62 (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 1708 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1439 time to evaluate : 5.840 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: 269 outliers final: 124 residues processed: 1620 average time/residue: 0.5650 time to fit residues: 1516.9970 Evaluate side-chains 1293 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1169 time to evaluate : 5.855 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 0 residues processed: 124 average time/residue: 0.4058 time to fit residues: 104.3235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 444 optimal weight: 1.9990 chunk 363 optimal weight: 0.2980 chunk 147 optimal weight: 0.9990 chunk 534 optimal weight: 5.9990 chunk 577 optimal weight: 5.9990 chunk 476 optimal weight: 9.9990 chunk 530 optimal weight: 4.9990 chunk 182 optimal weight: 0.4980 chunk 429 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 30 ASN ** 2 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 191 GLN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 85 ASN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN C 97 GLN C 98 GLN F 97 GLN O 143 GLN S 122 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 47096 Z= 0.224 Angle : 0.798 25.066 63588 Z= 0.389 Chirality : 0.046 0.240 7448 Planarity : 0.005 0.094 8162 Dihedral : 6.000 52.597 6608 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.17 % Rotamer Outliers : 3.40 % 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: -1.18 (0.10), residues: 5957 helix: 1.15 (0.11), residues: 2282 sheet: -1.25 (0.13), residues: 1372 loop : -2.50 (0.11), residues: 2303 *********************** REFINEMENT MACRO_CYCLE 3 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 1542 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1372 time to evaluate : 6.112 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 outliers start: 170 outliers final: 81 residues processed: 1461 average time/residue: 0.5619 time to fit residues: 1365.0337 Evaluate side-chains 1246 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1165 time to evaluate : 5.646 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 0.4083 time to fit residues: 70.3941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 0.0040 chunk 402 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 359 optimal weight: 1.9990 chunk 536 optimal weight: 0.9980 chunk 568 optimal weight: 9.9990 chunk 280 optimal weight: 0.0270 chunk 508 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 overall best weight: 0.5652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 191 GLN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN W 85 ASN W 88 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN Y 85 ASN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN A 62 ASN C 62 ASN C 68 GLN ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 125 GLN T 108 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 47096 Z= 0.202 Angle : 0.789 28.040 63588 Z= 0.382 Chirality : 0.045 0.220 7448 Planarity : 0.005 0.088 8162 Dihedral : 5.778 52.356 6608 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.61 % Favored : 94.28 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.83 (0.10), residues: 5957 helix: 1.46 (0.11), residues: 2282 sheet: -0.90 (0.15), residues: 1085 loop : -2.34 (0.10), residues: 2590 *********************** REFINEMENT MACRO_CYCLE 4 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 1486 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1322 time to evaluate : 5.748 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 outliers start: 164 outliers final: 81 residues processed: 1435 average time/residue: 0.5600 time to fit residues: 1337.4120 Evaluate side-chains 1249 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1168 time to evaluate : 5.581 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 0.4027 time to fit residues: 69.2795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 423 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 485 optimal weight: 9.9990 chunk 392 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 290 optimal weight: 4.9990 chunk 510 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 GLN Z 85 ASN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 85 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN 2 88 ASN H 85 ASN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN V 88 ASN I 85 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN W 88 ASN W 141 GLN J 85 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN L 85 ASN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 GLN A 62 ASN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN E 62 ASN F 62 ASN O 98 GLN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 158 ASN T 122 GLN T 158 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 47096 Z= 0.447 Angle : 0.902 28.867 63588 Z= 0.444 Chirality : 0.049 0.262 7448 Planarity : 0.005 0.101 8162 Dihedral : 6.070 55.689 6608 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.30 % Favored : 93.54 % Rotamer Outliers : 4.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.94 (0.10), residues: 5957 helix: 1.29 (0.10), residues: 2282 sheet: -1.18 (0.13), residues: 1344 loop : -2.25 (0.12), residues: 2331 *********************** REFINEMENT MACRO_CYCLE 5 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 1395 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1156 time to evaluate : 5.678 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 outliers start: 239 outliers final: 151 residues processed: 1313 average time/residue: 0.5629 time to fit residues: 1229.5814 Evaluate side-chains 1189 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1038 time to evaluate : 5.675 Switching outliers to nearest non-outliers outliers start: 151 outliers final: 0 residues processed: 151 average time/residue: 0.3968 time to fit residues: 122.0666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 5.9990 chunk 511 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 333 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 568 optimal weight: 4.9990 chunk 472 optimal weight: 0.6980 chunk 263 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN W 141 GLN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 88 ASN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN G 62 ASN R 98 GLN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 GLN T 125 GLN ** T 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 226 GLN ** U 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 47096 Z= 0.290 Angle : 0.833 27.650 63588 Z= 0.408 Chirality : 0.046 0.198 7448 Planarity : 0.005 0.098 8162 Dihedral : 5.932 54.753 6608 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.84 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.78 (0.11), residues: 5957 helix: 1.50 (0.11), residues: 2282 sheet: -1.09 (0.13), residues: 1316 loop : -2.25 (0.12), residues: 2359 *********************** REFINEMENT MACRO_CYCLE 6 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 1287 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1169 time to evaluate : 5.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 60 residues processed: 1239 average time/residue: 0.5728 time to fit residues: 1177.8484 Evaluate side-chains 1123 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1063 time to evaluate : 5.778 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.4127 time to fit residues: 54.4489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 324 optimal weight: 0.0870 chunk 415 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 chunk 478 optimal weight: 8.9990 chunk 317 optimal weight: 0.1980 chunk 566 optimal weight: 1.9990 chunk 354 optimal weight: 0.9990 chunk 345 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 overall best weight: 0.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN I 85 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN W 141 GLN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN B 23 GLN B 62 ASN C 62 ASN D 62 ASN D 125 GLN E 183 ASN R 98 GLN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 143 GLN U 143 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 47096 Z= 0.225 Angle : 0.830 26.766 63588 Z= 0.404 Chirality : 0.046 0.193 7448 Planarity : 0.005 0.100 8162 Dihedral : 5.793 54.665 6608 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.03 % Favored : 93.86 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.65 (0.11), residues: 5957 helix: 1.65 (0.11), residues: 2282 sheet: -1.07 (0.13), residues: 1232 loop : -2.17 (0.11), residues: 2443 *********************** REFINEMENT MACRO_CYCLE 7 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 1284 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1203 time to evaluate : 5.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 35 residues processed: 1253 average time/residue: 0.5723 time to fit residues: 1191.7693 Evaluate side-chains 1120 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1085 time to evaluate : 5.330 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3869 time to fit residues: 32.9122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 0.0870 chunk 226 optimal weight: 7.9990 chunk 338 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 360 optimal weight: 0.7980 chunk 386 optimal weight: 5.9990 chunk 280 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 445 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 88 ASN Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN 2 141 GLN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 GLN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN Y 141 GLN Y 191 GLN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN D 183 ASN E 62 ASN F 183 ASN R 98 GLN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 47096 Z= 0.221 Angle : 0.824 27.728 63588 Z= 0.401 Chirality : 0.045 0.212 7448 Planarity : 0.005 0.113 8162 Dihedral : 5.660 50.772 6608 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.89 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.64 (0.11), residues: 5957 helix: 1.73 (0.11), residues: 2275 sheet: -1.19 (0.13), residues: 1211 loop : -2.14 (0.11), residues: 2471 *********************** REFINEMENT MACRO_CYCLE 8 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 1273 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1201 time to evaluate : 5.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 31 residues processed: 1232 average time/residue: 0.5702 time to fit residues: 1160.3749 Evaluate side-chains 1124 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1093 time to evaluate : 5.389 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4238 time to fit residues: 31.7653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 0.0170 chunk 542 optimal weight: 4.9990 chunk 495 optimal weight: 9.9990 chunk 528 optimal weight: 0.9990 chunk 317 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 414 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 477 optimal weight: 1.9990 chunk 499 optimal weight: 3.9990 chunk 526 optimal weight: 5.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 36 GLN W 88 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 88 ASN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN Y 191 GLN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN G 62 ASN R 98 GLN S 125 GLN ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 47096 Z= 0.303 Angle : 0.866 25.936 63588 Z= 0.422 Chirality : 0.047 0.242 7448 Planarity : 0.005 0.110 8162 Dihedral : 5.757 51.150 6608 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.21 % Favored : 93.62 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.65 (0.11), residues: 5957 helix: 1.62 (0.11), residues: 2275 sheet: -1.00 (0.13), residues: 1267 loop : -2.18 (0.11), residues: 2415 *********************** REFINEMENT MACRO_CYCLE 9 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 1163 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1104 time to evaluate : 6.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 31 residues processed: 1132 average time/residue: 0.5883 time to fit residues: 1108.2954 Evaluate side-chains 1100 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1069 time to evaluate : 5.969 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4492 time to fit residues: 33.9362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 5.9990 chunk 558 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 388 optimal weight: 0.9990 chunk 585 optimal weight: 9.9990 chunk 539 optimal weight: 7.9990 chunk 466 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 360 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 88 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 191 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN A 125 GLN ** Q 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 GLN ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.6916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 47096 Z= 0.333 Angle : 0.898 26.284 63588 Z= 0.439 Chirality : 0.047 0.262 7448 Planarity : 0.005 0.117 8162 Dihedral : 5.866 52.507 6608 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.48 % Favored : 93.35 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.67 (0.11), residues: 5957 helix: 1.56 (0.11), residues: 2275 sheet: -0.98 (0.13), residues: 1225 loop : -2.14 (0.11), residues: 2457 ********************** REFINEMENT MACRO_CYCLE 10 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 1150 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1107 time to evaluate : 5.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 26 residues processed: 1128 average time/residue: 0.5859 time to fit residues: 1099.3641 Evaluate side-chains 1085 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1059 time to evaluate : 5.650 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4112 time to fit residues: 28.1217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 8.9990 chunk 496 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 430 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 467 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 479 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN H 36 GLN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN W 191 GLN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 GLN Y 88 ASN L 85 ASN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN D 125 GLN O 226 GLN ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 GLN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 226 GLN ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 226 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.122791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.103458 restraints weight = 84217.501| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.49 r_work: 0.3478 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work: 0.3458 rms_B_bonded: 3.26 restraints_weight: 0.1250 r_work: 0.3447 rms_B_bonded: 3.30 restraints_weight: 0.0625 r_work: 0.3436 rms_B_bonded: 3.38 restraints_weight: 0.0312 r_work: 0.3424 rms_B_bonded: 3.47 restraints_weight: 0.0156 r_work: 0.3413 rms_B_bonded: 3.58 restraints_weight: 0.0078 r_work: 0.3400 rms_B_bonded: 3.72 restraints_weight: 0.0039 r_work: 0.3388 rms_B_bonded: 3.87 restraints_weight: 0.0020 r_work: 0.3375 rms_B_bonded: 4.03 restraints_weight: 0.0010 r_work: 0.3361 rms_B_bonded: 4.22 restraints_weight: 0.0005 r_work: 0.3347 rms_B_bonded: 4.43 restraints_weight: 0.0002 r_work: 0.3333 rms_B_bonded: 4.66 restraints_weight: 0.0001 r_work: 0.3318 rms_B_bonded: 4.91 restraints_weight: 0.0001 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 47096 Z= 0.267 Angle : 0.878 25.568 63588 Z= 0.431 Chirality : 0.047 0.235 7448 Planarity : 0.006 0.126 8162 Dihedral : 5.814 51.978 6608 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.33 % Favored : 93.54 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.68 (0.11), residues: 5957 helix: 1.65 (0.11), residues: 2275 sheet: -1.14 (0.14), residues: 1211 loop : -2.17 (0.11), residues: 2471 =============================================================================== Job complete usr+sys time: 18240.03 seconds wall clock time: 324 minutes 18.44 seconds (19458.44 seconds total)